Package: aroma.affymetrix
=========================

Version: 3.2.2 [2024-02-18]

DOCUMENTATION:

 * Fix minor Rd help-page issues.


Version: 3.2.1 [2022-07-18]

PERFORMANCE:

 * MEMORY: Some parameter estimates where pre-allocated as logical (NA)
   values, instead of as numeric (NA_real_) values, which would result in
   an unnecessary coercion from logical to numeric.
 

Version: 3.2.0 [2019-06-22]

NEW FEATURES:

 * Windows Shortcut links (*.lnk) to CEL files are now also recognized
   as CEL files.
 
BUG FIXES:

 * findByChipType() for AffymetrixCdfFile and AffymetrixPdfFile would
   only recognize Windows Shortcut Links with a filename extension
   in lower case (*.lnk) but not in upper case (*.LNK).

 * TESTS: Package test on CEL files would produce an error on MS Windows
   if only Windows Shortcut links were supported but not symbolic links.
 

Version: 3.1.1 [2018-04-16]

SIGNIFICANT CHANGES:

 * Package requires R (>= 3.2.0) and BioC (>= 3.1) both released
   in April 2015.

BUG FIXES:

 * Removed invalid 'break' statement in getAlleleProbePairs() for
   AffymetrixCdfFile.

CODE REFACTORING:

 * Using indexByRow(dim(x)) internally since indexByRow(x) will soon be
   deprecated in matrixStats.
 
DEPRECATED AND DEFUNCT:

 * Passing argument 'ram' to any of the doNnn() methods is now defunct and
   gives an informative error message. It has been given a warning since
   v2.8.4 (May 2013).  Use setOption(aromaSettings, 'memory/ram', ram).

 * Monocell CDF files named with a very very old "-monocell.cdf" suffix are
   now ignored.  There has been an informative error that these are defunct
   since v 2.6.3 (October 2012).


Version: 3.1.0 [2017-03-23]

NEW FEATURES:

 * Now file and object sizes are reported using IEC binary prefixes,
   i.e. bytes, KiB, MiB, GiB, TiB, ..., YiB.

 * Now doNnn() methods can be called directly from the command line, e.g.
   Rscript -e aroma.affymetrix::doCRMAv2 --dataSet=HapMap270
   --chipType=GenomeWideSNP_6

 * Objects no longer report on memory (RAM) usage.

REFACTORIZATION:

 * Used partial element name 'coef' instead of 'coefficients' for lm() fit.
 
BUG FIXES:

 * Package used %<=% internally with was deprecated in future (>= 1.4.0).
 
 * ROBUSTNESS: Some regular expression patterns used for locating files
   would match any symbol when it intended to match only a period.
   
 * The International HapMap Project (http://www.hapmap.org/) is being retired
   and HTTP server http://hapmap.ncbi.nlm.nih.gov/downloads/raw_data/ is
   decomissioned. System test scripts updated to download HapMap CEL files
   from the FTP server ftp://ftp.ncbi.nlm.nih.gov/hapmap/raw_data/ instead.

DEPRECATED AND DEFUNCT:

 * Methods bgAdjustRma(), bgAdjustOptical() and bgAdjustGcrma() for
   AffymetrixCelFile as well as bgAdjustGcrma() for AffymetrixCelSet
   are now defunct.


Version: 3.0.0 [2016-01-09]

SIGNIFICANT CHANGES:

 * Package requires R (>= 3.1.2) and BioC (>= 3.0) both released
   in October 2014. 

NEW FEATURES:

 * REPRODUCIBILITY: GcRmaBackgroundCorrection(), LimmaBackgroundCorrection(),
   and RmaBackgroundCorrection() gained argument 'seed'.
  
 * REPRODUCIBILITY: Several of the methods now generate *.md5 checksum 
   files for the data files they output.
  
 * Now also convertToUnique() acknowledge asterisk tags.
  
PERFORMANCE:

 * SPEED: Adding support for parallel/distributed processing via futures
   to some of the methods for which it is possible to process each
   sample independently, e.g. background and crosstalk correction methods.

REFACTORIZATION:

 * ROBUSTNESS: Using do.call(fcn) internally instead of do.call("fcn").
  
 * CLEANUP: Warnings on "is.na() applied to non-(list or vector) of 
   type 'NULL'" are no longer generated.

SOFTWARE QUALITY:

 * ROBUSTNESS: MatNormalization did not create CEL files atomically.

BUG FIXES:

 * LimmaBackgroundCorrection(..., addJitter=TRUE) gave an error.
 
DEPRECATED AND DEFUNCT:

 * CLEANUP: Formally defunct'ed bgAdjustRma(), bgAdjustGcrma(), 
   bgAdjustOptical() for AffymetrixCelFile/AffymetrixCelSet since they
   have effectively been defunct'ed in the public API for years.  These
   are now all incorporated in corresponding BackgroundCorrection classes.
  
 
Version: 2.14.0-9000 [2015-12-23]
  
 * ROBUSTNESS: Using getPathname() instead of accessing private field.

BUG FIXES:

 * convertToUnique() for AffymetrixCelSet would give an error if there was
   an error while checking if results already exist.
 
 
Version: 2.14.0 [2015-10-24]
  
 * AvgPlm, used by for instance doCRMAv2(), would give harmless warning
   "Argument 'centers' for matrixStats::rowMads() has been renamed to
   'center'. Please update code accordingly."
   
 * ROBUSTNESS: fitCnProbes() for UnitModel could in rare cases give an
   error on one of the internal sanity checks.

SOFTWARE QUALITY:
  
 * ROBUSTNESS: Explicitly importing core R functions.
    
BUG FIXES:

 * extractAlleleSet() for SnpChipEffectSet now needs to load namspace
   'oligoClasses' explicitly.
  
 * writeCdf() for AffyGenePDInfo gave "Error in affxparser::writeCdf(...) :
   unused argument (pathname = ..." due to a bug/typo introduced in 2.13.2.
   Thanks to Guillaume Devailly for reporting on this.
 
DEPRECATED AND DEFUNCT:

 * Removed methods marked as defunct in v2.11.3 (Feb 2014).
  
 
Version: 2.13.2 [2015-05-26]

SIGNIFICANT CHANGES:
  
 * Package now requires R (>= 3.1.1) released July 2014. This allows
   us to use BioC (>= 3.0) (October 2014).

SOFTWARE QUALITY:
  
 * ROBUSTNESS: Many functions now assert that they don't return file
   data sets with duplicated entries.
  
 * ROBUSTNESS: Package now declares all S3 methods.
 
 
Version: 2.13.1 [2015-01-23]
  
 * Now a pre-existing monocell CDF can be recreated and overwritten
   using getMonocellCdf(cdf, force=TRUE).

BUG FIXES:

 * getMonocellCdf() for AffymetrixCdfFile would throw "Error in (...) : 
   3 arguments passed to '(' which requires 1".  This was due to a typo
   (erroneous newline) introduced in 2.13.0.  Add package tests for this.
   Thanks to Qingzhou Zhang for reporting on this.
 
 
Version: 2.13.0 [2015-01-17]
  
 * Bumped version for CRAN submission.
  
 * Updated package dependencies.
  
SOFTWARE QUALITY:
  
 * Package passes all redundancy tests.
 
 
Version: 2.12.10 [2015-01-06]
  
 * CLEANUP: Major cleanup of namespace imports from suggested packages
   such as affxparser and aroma.light.
 
 
Version: 2.12.9 [2014-11-17]
  
 * Updated redundancy tests under testScripts/ to find rowMedians() of
   the matrixStats package.  The matrixStats package used to be attached
   whenever aroma.light (< 2.1.1) was attached, but no longer.
 
 
Version: 2.12.8 [2014-09-04]

BUG FIXES:

 * ROBUSTNESS/BUG FIX: createFrom(..., mode="copy") for AffymetrixCelFile
   would give an error on "No permission to modify existing file: ..."
   iff the source file had read-only permission.  This bug was introduced
   by changes to base::file.copy() in R (>= 2.13.0) [April 2011].
   Thanks to Taylor Raborn at Indiana University for reporting on this.
 
 
Version: 2.12.7 [2014-08-27]
  
BUG FIXES:

 * Added forgotten NAMESPACE imports.
 
 
Version: 2.12.6 [2014-06-29]
  
BUG FIXES:

 * getAromaCellSequenceFile() for AffymetrixCdfFile used undefined variable
   'nbrOfCells'.
 
 
Version: 2.12.5 [2014-06-24]

SOFTWARE QUALITY:

 * Added package system tests utilizing example data of Bioconductor
   package AffymetrixDataTestFiles, iff installed.
 
 
Version: 2.12.4 [2014-06-09]

SIGNIFICANT CHANGES:
    
 * Package now requires R (>= 3.0.0) and BioC (>= 2.13), which were
   released April 2013 and are in fact old and it's recommended to
   use a more recent version of R.
  
 * Added 'SuggestsNote' field to DESCRIPTION with list of packages
   that are recommended for the most common use cases.
  
 * Bumped package dependencies.
 
 
Version: 2.12.3 [2014-05-02]
  
 * CLEANUP: Now using ds[[idx]] instead of getFile(ds, idx) where possible.
 
 
Version: 2.12.2 [2014-04-28]
  
 * Added justRMA() for AffymetrixCelSet, which with good precision
   reproduces the results of the default setting of justRMA() in the
   affy package.  It does so by still running with a constant memory
   profile.  This means that a much larger number of samples can be
   processed using this implementation.
  
 * doCRMAv2(..., drop=FALSE) and hence doASCRMAv2(..., drop=FALSE), did
   not *return* the base-position normalization step, although it was
   done and its outcome was part of all downstream steps.
  
 * extractExpressionSet() for ChipEffectSet gained argument 'orderUnitsBy'
   and returns standard errors as well.
 
 
Version: 2.12.1 [2014-04-26]
  
 * SPEEDUP: Minor speedup by replacing repetive <ns>::<fcn>() calls
   with repetive <fcn>() calls; the '::' operator is fairly expensive.
   You should expect a small speed improvement when using MatSmoothing(),
   RmaPlm(..., flavor="oligo") and when calculating weights using
   ExonRmaPlm and QualityAssessmentModel, to name a few examples.
 
 
Version: 2.12.0 [2014-03-07]
  
 * Bumped version for CRAN submission.
  
 * Updated package dependencies.

SOFTWARE QUALITY:

 * Package passes all redundancy tests.
 
 
Version: 2.11.3 [2014-02-28]
  
 * Now methods that supports searching sibling root directories do so by
   default.  Previously this had to be explicitly enabled via an option.

DEPRECATED AND DEFUNCT:

 * CLEANUP: Removed defunct methods.  Made previously deprecated defunct.
 
 
Version: 2.11.2 [2014-01-04]
  
DEPRECATED AND DEFUNCT:

 * CLEANUP: Dropped defunct methods '[' and '[[' for AffymetrixCelSet
   and CnagCfhSet (which have been defunct since 2013-04-29).
 
 
Version: 2.11.1 [2013-10-17]
  
 * DOCUMENTATION: Minor tweaks to the help for the doNNN() methods.
 
 
Version: 2.11.0 [2013-10-17]

SIGNIFICANT CHANGES:

 * Package now requires R (>= 2.15.0) [and Bioc (>= 2.10.0)].

 * Updated package dependencies.
 
 
Version: 2.10.3 [2013-10-07]
  
 * CLEANUP: No longer need to attach R.utils for backward compatibility.
  
 * CLEANUP: Package no longer apply downloaded package patches.
  
 * CLEANUP: Now explicitly importing only what is needed in NAMESPACE.
  
 * CLEANUP: No longer uses ':::' for accessing 'oligo' functions.
  
 * Updated package dependencies.
 
DEPRECATED AND DEFUNCT:

 * CLEANUP: Deprecated patch() for AromaAffymetrix.
  
 
Version: 2.10.2 [2013-09-28]
  
 * Now the 'aroma.affymetrix' Package object is also available when the
   package is only loaded (but not attached).
  
 * Updated package dependencies.
 
 
Version: 2.10.1 [2013-08-21]
  
 * Now explicitly importing R.filesets and aroma.core in NAMESPACE.
 
 
Version: 2.10.0 [2013-08-04]
  
 * CLEANUP: The formal package dependency on Bioconductor packages
   'aroma.light' and 'affxparser' has been relaxed so the package
   can be installed without them.
  
 * CLEANUP: Package now only imports matrixStats, R.oo, R.filesets
   and aroma.apd.
  
 * Bumped version for CRAN submission.
  
 * Updated package dependencies.

SOFTWARE QUALITY:

 * Package passes all redundancy tests.
 
DEPRECATED AND DEFUNCT:

 * CLEANUP: Removed since-long defunct methods.  Made deprecated
   methods defunct.
  
 
Version: 2.9.7 [2013-07-28]
  
 * ROBUSTNESS: byPath() for DChipDcpSet was not declared static.
  
BUG FIXES:

 * In certain cases, calls to static method byPath() would be affected by the
   NextMethod() '...' bug reported in R-devel thread "Do *not* pass '...' to 
   NextMethod() - it'll do it for you; missing documentation, a bug or just 
   me?" on 2012-10-16.
 
 
Version: 2.9.6 [2013-07-03]
  
 * Added argument 'flavor' or doRMA() making it easier to replicate the
   results of other packages, e.g. doRMA(..., flavor="oligo").
 
 
Version: 2.9.5 [2013-06-02]
  
 * ROBUSTNESS: Now more methods are creating/writing signals atomically.
  
BUG FIXES:

 * Since v2.9.0, doFIRMA() would give "Exception: Unknown arguments: 
   .onUnknownArgs" in the alternative splicing step.
  
 * calculateConfidenceScores() for CrlmmModel used defunct method
   isHeterozygote() instead of isHeterozygous().
  
 * Certain methods could throw 'Error in UseMethod("getChecksum"): no
   applicable method for 'getChecksum' applied to an object of class "list"'
   if (and only if) R.cache package was not attached.  The same bug was
   fixed on aroma.core v2.9.2 recently.
 
 
Version: 2.9.4 [2013-05-30]
  
 * Now it's possible to call aroma.affymetrix::doRMA() without first
   loading package.  Same for all other doNnn() methods, e.g. doCRMAv2(),
   doFIRMA() and doGCRMA().
 
 
Version: 2.9.3 [2013-05-25]
  
 * SPEEDUP: Replaced all rm() calls with NULL assignments.
 
 
Version: 2.9.2 [2013-05-22]
  
 * CLEANUP: Now using getChecksum() instead of (internal)
   R.filesets::digest2() with identical results.
  
 * CLEANUP: Now getIdentifier() for CnagCfhFile utilizes
   getChecksum() for the GenericDataFile class.
 
 
Version: 2.9.1 [2013-05-20]
  
SOFTWARE QUALITY:

 * CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.
 
 
Version: 2.9.0 [2013-05-02]
  
 * Submitted to CRAN.
  
SOFTWARE QUALITY:

 * The package passes all redundancy tests.
 
 
Version: 2.8.4 [2013-05-02]
  
 * DOCUMENTATION: Now doRMA(), doGCRMA(), doFIRMA(),
   doCRMAv1()/doASCRMAv1() and doCRMAv2()/doASCRMAv2() are
   fully documented and listed in the help index.
  
 * Added argument 'annotationPkg' to extractExpressionSet() for
   ChipEffectSet, which (indirectly) sets the 'annotation' slot
   of the returned ExpressionSet.
  
 * Added extractFeatureSet() for AffymetrixCelSet.
  
 * SPEEDUP: Added ^Cyto.*Array$ to list of SNP chips that isSnpChip()
   for AffymetrixCdfFile knows of without having to scan the CDF.
  
 * SPEEDUP: Just as doCRMAv2()/doASCRMAv2(), now also doRMA() and
   doGCRMA() return much quicker if already processed.
  
DEPRECATED AND DEFUNCT:

 * CLEANUP: Removed argument 'ram' from doNnn() methods in favor
   setOption(aromaSettings, 'memory/ram', ram).

 * CLEANUP: Made several deprecated methods defunct.
 
 
Version: 2.8.3 [2013-04-01]
  
 * Force creation of a generic process(), because depending on the
   version of R.rsp at the time of the build, process() may be missing
   or not.
  
 * Bumped up package dependencies.
 
 
Version: 2.8.2 [2013-03-22]
  
 * Obscufated the error message on ASCII CDFs on how to change settings
   to allow the processing of such, because it shouldn't be easy to
   do that.
 
 
Version: 2.8.1 [2013-03-05]
  
 * DOCUMENTATION: Updated the help usage section for all static methods.
  
 * Bumped up package dependencies.
 
 
Version: 2.8.0 [2012-12-21]
  
 * No updates.
  
 * Bumped version for CRAN submission.
  
SOFTWARE QUALITY:

 * Package passes all redundancy tests.
 
 
Version: 2.7.9 [2012-12-21]
  
 * Bumped package dependencies.
  
 * Utilizing new startupMessage() of R.oo.
  
 * ROBUSTNESS: Now all internal pathnames are shorter than 100
   characters, which is the upper limit that 'tar' supports.
 
DEPRECATED AND DEFUNCT:

 * Now using argument 'colClasses' (was 'colClassPatterns')
   for all readDataFrame():s and elsewhere.
  
 
Version: 2.7.8 [2012-12-18]
  
 * ROBUSTNESS: Added argument 'unitsBy' (and 'namesBy') to writeCdf()
   for AffyGenePDInfo, where 'unitsBy' defaults to "transcript".  It
   now also drops any duplicated probe entries.  Furthermore, calling
   writeCdf() for other classes of DBPDInfo objects will now give a
   more informative error message that those classes are yet not
   supported.  Thanks Guido Hooiveld (Wageningen University, Netherlands)
   for suggestions and tests.
  
 * Now validate() for AffymetrixCdfFile accepts empty unit names as
   long as the unit is not empty.
  
BUG FIXES:

 * writeCdf(..., useTranscriptCluster=FALSE) for AffyGenePDInfo could
   generate empty unit names files for units with 'fsetid' <= 9999.
 
 
Version: 2.7.7 [2012-12-10]
  
BUG FIXES:

 * getTimestamp() for AffymetrixCelFile would throw an error if the CEL file
   header did not have a timestamp.  Thanks Guido Hooiveld (Wageningen
   University, Netherlands) for reporting this.
 
 
Version: 2.7.6 [2012-12-06]
  
 * ROBUSTNESS: Utilizing new getOneFile() internally.
 
 
Version: 2.7.5 [2012-12-01]
    
BUG FIXES:

 * BUG FIX/ROBUSTNESS: convertToUnique() for AffymetrixCelSet would
   return all CEL files found in the output directory, not just the ones
   corresponding to the input set, and possibly in a different order.
 
 
Version: 2.7.4 [2012-11-29]
  
 * DOCUMENTATION: Added help pages to more methods.
  
 * ROBUSTNESS: updateUnits() for ResidualSet did not update the files in
   lexicographic order as previously claimed.
 
 
Version: 2.7.3 [2012-11-28]
  
 * ROBUSTNESS: Added system test scripts for building UGP and UFL
   file from Affymetrix CSF and NetAffx CSV files for GenomeWideSNP_6.
  
BUG FIXES:

 * Static allocateFromCdf() for AromaUfcFile and AromaUflFile would throw
   errors on "Cannot retrieve writable file/directory because it is NA.".
   This turns out to be related to the trap reported in R-devel thread
   'Do *not* pass '...' to NextMethod() - it'll do it for you; missing
   documentation, a bug or just me?' on Oct 16, 2012.  Thanks Ioana
   Cutcutache (Duke-NUS in Singapore) for reporting on this.
 
 
Version: 2.7.2 [2012-11-28]
  
 * ROBUSTNESS: Added the FileCacheKeyInterface to all classes directly
   extending GenericDataFile and TabularTextFile.
  
 * MEMORY: readUnits() for ChipEffectFile, FirmaFile, ParameterCelFile,
   ResidualFile, and WeightsFile no longer cache results in memory
   by default.
 
 
Version: 2.7.1 [2012-11-26]
  
 * Lowered the package dependencies to aroma.light (>= 1.22.0)
   and affxparser (>= 1.26.4) so that this package can be easily
   installed on R (>= 2.14.0).
 
 
Version: 2.7.0 [2012-11-24]
  
 * Bumped version for CRAN submission.
  
 * Bumped up package dependencies.
  
SOFTWARE QUALITY:

 * Package passes all redundancy tests.
 
 
Version: 2.6.16 [2012-11-21]
  
 * Updated verbose output of parameters.
 
 
Version: 2.6.14 [2012-11-21]
  
 * DOCUMENTATION: Hiding more internal methods from the help indices.
  
 * CLEANUP: Now utilizing the new ParametersInterface.
  
 * CLEANUP: Replaced all getParameterSet() with getParameters().

 * CLEANUP: bgAdjustGcrma() for AffymetrixCelSet no longer reads
   and write probe affinity files in the deprecated APD format.
  
 * CLEANUP: Removed obsolete code from internal bgAdjustOptical() that
   was never reached and that loaded affinities via obsolete APD files.
  
DEPRECATED AND DEFUNCT:
  
 * CLEANUP: bgAdjustOptical() and bgAdjustRma() for AffymetrixCelSet
   are now defunct.  Instead, see OpticalBackgroundCorrection and
   RmaBackgroundCorrection.
  
 * CLEANUP: Deprecated "[" and "[[" for AffymetrixCelFile,
   AffymetrixCelSet, CnagCfhFile, and CnagCfhSet.
 
 
Version: 2.6.13 [2012-11-18]
  
 * Now package explicitly imports R.cache, because aroma.core is no
   longer loading it.
 
 
Version: 2.6.12 [2012-11-14]
  
 * CLEANUP: getWeights() for QualityAssessmentModel no longer sets the
   alias of the returned data set, because the use of aliases is deprecated.
  
 * CLEANUP: writeImage() for AffymetrixCelFile no longer supports
   sample name aliases.
 
 
Version: 2.6.11 [2012-11-13]
  
 * CLEANUP: Properly declared all cached fields, making it possible
   to remove nearly all clearCache() implementations because the one
   for Object takes does the job.
 
 
Version: 2.6.10 [2012-11-12]
  
 * CLEANUP: Now seq_along(x) instead of seq(along=x) everywhere.
   Similarly, seq(ds) where 'ds' is GenericDataFileSet is now
   replaced by seq_along(ds).  Likewise, seq_len(x) replaces
   seq(length=x), and length(ds) replaces nbrOfFiles(ds).
 
 
Version: 2.6.9 [2012-11-08]
  
 * Renamed getColumnNames() to getDefaultColumnNames() for all
   classes inheriting from GenericTabularFile, because of the
   new ColumnNamesInterface interface.
 
 
Version: 2.6.8 [2012-11-05]
  
 * CLEANUP: Replaced all whichVector() with which(), because the
   latter is now the fastest again.
 
 
Version: 2.6.7 [2012-10-29]
  
 * CLEANUP: Now using Arguments$get(Read|Writ)ablePath() instead of
   filePath(..., expandLinks="any").
 
 
Version: 2.6.6 [2012-10-21]
  
 * ROBUSTNESS: Now using Arguments$getWritablePath() everywhere instead
   of mkdirs(), because the former will do a better job in creating
   and asserting directories on slow shared file systems, and when it
   fails it gives a more informative error message.
 
 
Version: 2.6.5 [2012-10-18]
  
 * ROBUSTNESS: Now createMonocellCdf() for AffymetrixCdfFile validates
   the CDF (via new validate()).  This will give more informative
   error message in case the CDF is invalid, e.g. containing "empty"
   units.
  
 * ROBUSTNESS: Added validate() for AffymetrixCdfFile, which validate
   a CDF for the most "common" errors, to help troubleshooting.  Note
   that the validation is not complete, i.e. rare/unknown errors are
   not caught.
  
 * Now as.character() for all AromaChipTypeAnnotationFile classes,
   and hence print(), reports the file size both as abbreviated as
   well as in exact number of bytes, e.g. "24.66 MB (25853850 bytes)"
   (used to only be "24.66 MB").
 
 
Version: 2.6.4 [2012-10-16]

BUG FIXES:

 * ROBUSTNESS/BUG FIX: No longer passing '...' to NextMethod(), cf.
   R-devel thread 'Do *not* pass '...' to NextMethod() - it'll do it
   for you; missing documentation, a bug or just me?' on Oct 16, 2012.
 
 
Version: 2.6.3 [2012-10-14]
  
 * CLEANUP: Moved AromaUnitGcContentFile to aroma.core.

DEPRECATED AND DEFUNCT:
  
 * CLEANUP: Removed several defunct/obsolete methods and turned
   deprecated methods into defunct/obsolete ones.
  
 * CLEANUP: findByChipType() for AffymetrixCdfFile no longer support
   monocell CDF file named <chipType>-monocell.CDF, and gives an
   informative error if that is still the case.  Since December 2007,
   the filename should instead be <chipType>,monocell.CDF.
  
 * CLEANUP: createParamCdf() for ChipEffectFile and FirmaFile no longer
   support '<chipType>-monocell' filenames.  If detected, an informative
   error is thrown.
 
 
Version: 2.6.2 [2012-09-15]
  
BUG FIXES:

 * doCRMAv2() failed to quickly located already available results if the
   chip type of the CDF had tags, e.g. 'GenomeWideSNP_6,Full'.
 
 
Version: 2.6.1 [2012-09-14]
  
 * MEMORY: Now getUnitIntensities() and readUnits() for AffymetrixCelSet
   no longer cache the results in memory if argument 'units' is NULL.
  
 * CLEANUP: Restructured part of the test scripts tree.  Added a new
   batch launcher.
  
BUG FIXES:

 * BUG FIX/ROBUSTNESS: Although getUnitIntensities() for AffymetrixCelSet
   would retrieve the CDF tree structure and pass it to affxparser's
   readCelIntensities(), it was done in such a way that the latter would
   still need to find and read the CDF.  This meant that it would not
   necessarily retrieve the same CDF as the AffymetrixCelSet used.
  
 * The utility function for downloading individual CEL files from GEO would
   give an error that it could not gunzip the downloaded file, iff the
   filename extension was lower case, e.g. *.cel.gz instead of *.CEL.gz.
 
 
Version: 2.6.0 [2012-09-05]
  
 * Submitted to CRAN.

SOFTWARE QUALITY:

 * The package passes all redundancy tests.
 
 
Version: 2.5.11 [2012-09-05]
  
 * ROBUSTNESS: Now doCRMAv1() adds also tag "v1" to the allele-specific
   calibration step.  The reason for this is to differentiate it from
   the output of doCRMAv2().  NOTE: This update means that any old CRMAv1
   analyzes will not be detected by doCRMAv1(); to have doCRMAv1() detect
   those add tag "v1" in that calibration step, e.g. "ACC,-XY,v1".
  
 * ROBUSTNESS: Now the CrlmmModel constructor asserts that the chip
   effects were estimated without merging the strands (mergeStrands=FALSE).
   If not, an informative exception is thrown.
 
 
Version: 2.5.10 [2012-09-04]

SOFTWARE QUALITY:

 * CLEANUP/ROBUSTNESS: Updated test scripts by rewriting some tests
   to be more clear/consistent on what they are testing and by
   cleaning out tests that duplicates each other etc.

 * Added system test scripts that automatically download the needed
   test data sets and install some extra packages needed for some
   of the tests.
  
BUG FIXES:

 * BUG FIX/ROBUSTNESS: extractAlleleSet(), extractSnpCnvQSet() and
   extractSnpQSet() for SnpChipEffectSet would throw an exception
   iff the 'Biobase' package was not loaded.
 
 
Version: 2.5.9 [2012-08-31]

SOFTWARE QUALITY:

 * Added system test scripts that automatically download the needed
   annotation data files iff missing.  This simplifies running the
   package's system tests on a new system.
 
 
Version: 2.5.8 [2012-08-30]

 * CLEANUP: Package no longer masks boxplot.stats(), getPackageName()
   and write() from other packages.
  
 * CLEANUP: Dropped system tests that did not test what other
   tests already test.
 
DEPRECATED AND DEFUNCT:
  
 * CLEANUP: Dropped readCdfDataFrame(), which is identical to
   the one in affxparser, which has remained the same since
   affxparser v1.21.1 (Oct 2010).
  
 
Version: 2.5.7 [2012-08-28]
  
 * SPEED UP: Now doCRMAv2() returns even faster if already processed.

SOFTWARE QUALITY:

 * Added systems test for running doASCRMAv2() in parallel using parLapply().
 
 
Version: 2.5.6 [2012-08-21]
  
 * CLEANUP: getRlmFitFunctions() no longer falls back to affyPLM, which
   was really only needed back in 2007.
  
DEPRECATED AND DEFUNCT:

 * CLEANUP: Dropped support for obsolete RmaPlm(..., flavor="affyPLMold").
  
 * CLEANUP: Now RmaPlm(..., flavor="oligo") no longer supports
   oligo (< 1.7.19), which can be considered obsolete version by now.
 
 
Version: 2.5.5 [2012-08-18]
  
 * Added argument 'useTranscriptCluster' to writeCdf() for AffyGenePDInfo.
 
 
Version: 2.5.4 [2012-06-21]
  
 * CLARIFICATION: Restructured the bpmapCluster2Cdf() method such that
   is more clear how BPMAP sequences are filtered out, i.e. keeping
   sequencing with a matching group name and excluding those that
   appears to be non-genomic control sequences.
  
 * ROBUSTNESS: Arguments 'rows' and 'cols' for bpmapCluster2Cdf() are
   mandatory (again).  The reason for this is that the BPMAP file is only
   useful to infer a lower bound for them, but not their exact values.
  
 * Added argument 'path' to bpmapCluster2Cdf(), which now defaults to
   annotationData/chipTypes/<chipType>/.
    
BUG FIXES:

 * bpmapCluster2Cdf() would exclude all units that had a probe starting at
   the very first position of a BPMAP sequence, because it interpreted that
   (incorrectly) as being a non-genomic control sequence.  This made no
   difference on some tiling arrays, but for others it dropped almost
   everything in the BPMAP file, e.g. Dm_tiling2_MR_v01.bpmap.  Thanks
   Hanat T, Heidelberg for reporting.
  
 * bpmapCluster2Cdf(..., minNbrOfProbes=n) filtered out units with less than
   (n+2L) probes, not n probes as documented.
  
 * bpmapCluster2Cdf() would write the incorrect 'unitnumber' in the CDF units
   (it was using the BPMAP sequence index).  This bug should have no impact
   on analysis in the Aroma framework, because that CDF field is ignored.
 
 
Version: 2.5.3 [2012-06-18]

 * FIX: Fixed a typo in an error message generated by byChipType()
   for AromaChipTypeAnnotationFile.
 
 
Version: 2.5.2 [2012-06-15]
  
 * Now writeCdf() for AffyGenePDInfo returns the pathname of the CDF.
  
 * Added trial version of class AffymetrixPgfFile.

SOFTWARE QUALITY:

 * ROBUSTNESS: Added a full system test for CalMaTe.
 
 
Version: 2.5.1 [2012-03-28]
  
 * Now convertToUnique() for AffymetrixCelSet skips already processed
   files in partially processed data sets.  Previously it would give
   an error if only some output files existed.
 
 
Version: 2.5.0 [2012-03-25]
  
 * Submitted to CRAN.

SOFTWARE QUALITY:
  
 * The package passes all redundancy tests.
 
 
Version: 2.4.3 [2012-03-23]
  
 * CRAN POLICY: Package no longer utilizes .Internal() calls.
  
DEPRECATED AND DEFUNCT:

 * CLEANUP: Deprecated PdInfo2Cdf() in favor (identical) pdInfo2Cdf(),
   because the former does not follow the Aroma naming conventions.
 
 
Version: 2.4.2 [2012-03-06]
  
 * GENERALIZATION: The new ArrayExplorer v3.4 will work with most
   commonly used web browsers including Mozilla Firefox, Google Chrome,
   Microsoft Internet Explorer, Apple Safari, and Opera.
  
 * CRAN POLICY: Started to remove .Internal() calls.
 
 
Version: 2.4.1 [2012-01-14]
  
 * ROBUSTNESS: Now the fit function of MbeiPlm gives an error
   whenever one tries to use prior parameters, which are yet
   not supported.
  
 * Updated getFitUnitGroupFunction() for RmaPlm to support prior
   probe-affinity parameters.
  
 * Added argument 'listOfPriors' to MultiArrayUnitModel(). Such
   priors are passed to the internal fitUnit() method.
  
 * Now validate() of MultiArrayUnitModel accepts single-array data
   sets, iff priors are set.
 
 
Version: 2.4.0 [2012-01-11]
  
 * ROBUSTNESS: Updated package dependencies.

SOFTWARE QUALITY:

 * Adapted a few redundancy tests for the most recent updates.
  
BUG FIXES:

 * fit() for ProbeLevelModel would throw an error due to a sanity check on
   unit dimensions that was only valid in certain cases.
 
 
Version: 2.3.5 [2011-11-20]
  
 * SPEEDUP: Constructor for AllelicCrosstalkCalibration no longer calls
   the very slow hasUnitTypes() for AffymetrixCdfFile, but instead only
   the much faster getUnitTypes().
  
 * Now byChipType() for AromaChipTypeAnnotationFile gives an error
   message with more information on which file it failed to locate,
   e.g. by specifying filename extension it looked for.
  
 * Added abstract getDefaultExtension() for AromaChipTypeAnnotationFile.
  
BUG FIXES:

 * Internally justSNPRMA() for AffymetrixCelSet would pass argument
   'verbose=log' instead of 'verbose=verbose', which would throw an error
   unless 'log' was assigned to be a logical value or a Verbose object.

DEPRECATED AND DEFUNCT:

 * CLEANUP: Deprecated doCRMA(). Use doCRMAv1() or doCRMAv2() instead.
  
 
Version: 2.3.4 [2011-11-18]
  
 * Now fit() for ProbeLevelModel fits one type of units at the time,
   which in turn is fitted in chunks of units with equal number of
   groups and cells per groups (very small chunks are merged together).
   Doing so will eventually allow us to speed up the restructuring of
   the data when reading signals and writing parameter estimates.
  
 * ROBUSTNESS: Added validation of argument 'fields' to readRawData()
   of AffymetrixCelFile and more internal sanity checks in that method.
 
 
Version: 2.3.3 [2011-11-11]
  
 * Now fit() for ProbeLevelModel fits one type of units at the time.
   For each unit type, the fitting is done in chunks.  The timing
   statistics presented in the verbose output is now per unit type.
   The purpose of this is to move toward fitting in chunks of units
   where the units are all of the same type and dimension (number
   of groups and number of cells per group).

SOFTWARE QUALITY:
  
 * Added more system tests.
 
 
Version: 2.3.2 [2011-11-10]
  
 * Added doFIRMA().
  
 * ROBUSTIFICATION: Now FirmaModel(plm) asserts that 'plm' is an
   ExonRmaPlm object (before any ProbeLevelModel would work), and
   that the PLM is setup for transcripts (mergeGroups=TRUE), not exons.
  
 * SPEEDUP: Now the internal fit functions of FirmaModel utilizes
   the 'matrixStats' package.  Also cleaned out some unnecessary calls.
  
 * ROBUSTNESS: doGCRMA() is now guaranteed to undo any changes of
   the CDF of the data set, e.g. if there is a user interrupt.
 
 
Version: 2.3.1 [2011-11-05]
  
 * FIX: The verbose enter/exit statements of fit() of CrlmmModel()
   did not match up, resulting deeper and deeper indentations.
 
 
Version: 2.3.0 [2011-10-28]
  
 * Added a namespace to the package, which will be more or less
   a requirement starting with R v2.14.0.
  
 * Added Bioconductor package 'AffymetrixDataTestFiles' to the list
   of suggested package, just to remove one R CMD check "NOTE".
 
 
Version: 2.2.3 [2011-09-29]

SOFTWARE QUALITY:
  
 * Added more system tests.
 
 
Version: 2.2.2 [2011-09-17]
  
 * Added writeCdfByExcludingCells() for AffymetrixCdfFile.
 
 
Version: 2.2.1 [2011-09-11]
  
 * Added createExonByTranscriptCdf() for creating exon-by-transcript CDFs.
   This methods was adapted from the createTranscriptCDF(), which was
   previously provided online.
  
 * Added a build script for createExonByTranscriptCdf() on HuEx-1_0-st-v2.
  
 * Added getHeaderAttributes() for AffymetrixNetAffxCsvFile which is
   used by new getGenomeBuild(), getNetAffxBuild() and getNetAffxDate().
 
 
Version: 2.2.0 [2011-09-01]
  
 * Submitted to CRAN.

SOFTWARE QUALITY:

 * The package passes all redundancy tests.
 
 
Version: 2.1.9 [2011-08-31]
  
 * Added bpmapCluster2Cdf(), which is a pruned and robustified version
   of ditto previously provided by Mark Robinson online.  This new
   version includes more sanity checks and avoids overwriting existing
   CDF files.
  
 * ROBUSTNESS: Now env2Cdf() writes the CDF file atomically by first
   writing to a temporary file which is then renamed.  It now also
   returns the pathname to the CDF written.
  
BUG FIXES:

 * ROBUSTNESS: getTimestamp() for AffymetrixCelFile would throw "Error in if
   (hasTimestamp) { : argument is of length zero" if the CEL file had a DAT
   header with a non-standard chip type string, e.g. an early-access label or
   no label at all.  Updated the local/inner  getTimestampFromDatHeader() of
   getTimestamp() to also handle such CEL files.  Thanks Irina Ostrovnaya
   at MSKCC for reporting on this.
 
 
Version: 2.1.8 [2011-08-16]
  
 * ROBUSTNESS: If static byName() for AffymetrixCelSet fails to setup
   a data set, it now reports the error message for each data set
   directory it tried.
 
 
Version: 2.1.7 [2011-08-08]
  
 * WORKAROUND: Added similar workarounds as in v2.1.6 for more methods
   defined in aroma.core, apply(), rowSums() etc.
 
 
Version: 2.1.6 [2011-07-27]
  
 * WORKAROUND: In order for the package to work with the most recent
   version of R devel, which automatically add namespaces to packages
   who do not have one, we explicitly have specify that this package
   should get function such as cat() and getOption() from R.utils
   (instead of 'base').
 
 
Version: 2.1.5 [2011-07-24]
  
 * Bumped up the package dependencies, especially since R will
   soon (in practice) require namespaces for all packages.
 
 
Version: 2.1.4 [2011-07-14]
  
 * Added extractExpressionSet() for ChipEffectSet.
  
 * ROBUSTNESS: Added redundancy tests for doRMA() and
   extractExpressionSet() for the HG-U133_Plus_2 chip type.
 
 
Version: 2.1.3 [2011-06-07]
  
 * ROBUSTNESS: Now the search path is adjusted such that 'ggplot2' comes
   after 'aroma.affymetrix', because the former overrides the generic
   rescale() function of the latter with a non-generic function.
 
 
Version: 2.1.2 [2011-05-26]
  
 * Added an archive of scripts used to build ACS, UGP and UFL annotation
   files.  The archive is located under buildScripts/ of the package
   installation directory and sorted by chip types.
 
 
Version: 2.1.1 [2011-04-18]
  
 * DOCUMENTATION: Added more help to createUniqueCdf() for AffymetrixCdfFile.
    
 * More updates to readGeneAssignments() for AffymetrixNetAffxCsvFile.

DEPRECATED AND DEFUNCT:

 * DEPRECATED: getUnique() and createUnique() are deprecated.
   Use getUniqueCdf() and createUniqueCdf() instead.

 * CLEANUP: Dropped argument 'sep' of createMonocellCdf() and
   createUniqueCdf() for AffymetrixCdfFile.
 
 
Version: 2.1.0 [2011-04-08]
  
 * No updates.  Submitted to CRAN.
 
 
Version: 2.0.10 [2011-04-07]
  
 * Added argument 'drop' to doRMA(), doGCRMA(), doCRMAv1(), and
   doCRMAv2().  If FALSE, all intermediate data sets and models are
   returned in a named list, otherwise only the final data set(s).
  
 * Added argument 'uniquePlm' to doRMA() and doGCRMA() for doing
   probe-level summarization on unique probe sets only.
  
 * Added readGeneAssignments() for AffymetrixNetAffxCsvFile.
  
 * CLEANUP: Utilizing hpaste() internally wherever applicable.

SOFTWARE QUALITY:
  
 * Package passes all system tests.
 
 
Version: 2.0.9 [2011-03-26]
  
 * ROBUSTNESS: Now internal bgAdjustGcrma(..., type="affinities") for
   AffymetrixCelFile gives a more informative error message when there
   are too few negative controls.
 
 
Version: 2.0.8 [2011-03-14]
  
 * doRMAv1() and doCRMAv2() gained argument 'lengthRange', which is
   passed to the constructor of FragmentLengthNormalization.
  
 * SPEEDUP: Added MOUSEDIVm520650 to the set of predefined chip types
   in AllelicCrosstalkCalibration.
 
 
Version: 2.0.7 [2011-03-10]
  
BUG FIXES:

 * append() for AffymetrixCelSet:s would throw 'Error in base::append(
   this$files, files, ...) : unused argument(s) (other = NA)'.  Added a
   redundancy test.  Thanks Ajanthah Sangaralingam at Queen Mary,
   University of London, for reporting on this.
 
 
Version: 2.0.6 [2011-03-04]
  
 * ROBUSTNESS: Now getCellIndices() for AffymetrixCdfFile asserts that
   argument 'units' can be coerced to integer indices.  Also, after
   correcting a bug in lapplyInChunks() of aroma.core, getCellIndices()
   now correctly returns an empty set if argument 'units' is integer(0).
 
 
Version: 2.0.5 [2011-03-03]
  
 * GENERALIZATION: Now AffymetrixCelSet and CnagCfhSet locates sample
   annotation files and sets the attributes following the new aroma
   search convention, i.e. by first loading *.saf files from
   main root path annotationData/ and then from optional sibling root
   paths annotationData,<tags>/.
  
 * ROBUSTNESS: QuantileNormalization now saves normalized data
   atomically, which lowers the risk for generating incomplete/corrupt
   data files.
  
 * ROBUSTNESS: Added a return contract/sanity check asserting that
   getUnitsOnChromosomes() for GenomeInformation truly returns valid
   'unit' indices.  Thanks to Emilie Sohier, France for reporting
   on a problem related to this.
 
 
Version: 2.0.4 [2011-03-01]
  
 * GENERALIZATION: Now getAverageFile() and getBaseline() first try to
   locate an existing result file in one of the root paths.
   If not found, a new one is created.
  
 * GENERALIZATION: Now byName() for AffymetrixCelSet tries to setup all
   data set directories matching the query and not just the first one.
   It also requires that the data sets found by byPath() are
   non-empty, otherwise they are skipped.
  
 * STANDARDIZATION: Now the default output path for all allocateFromCdf()
   is annotationData/chipTypes/<chipType>/.  Before it was the same
   directory as the CDF, which may for instance have been in a deeper
   subdirectory, or recently also in a sibling root path.
  
 * CLEAN UP: Harmonized all code for allocating/writing atomically,
   where we first write to a temporary file which is then renamed.
 
 
Version: 2.0.3 [2011-02-24]
  
 * GENERALIZATION: Starting to add support for locating data sets in
   root paths that also have tags, e.g. rawData/ and rawData,shared/.
   When this is in place, it will simplify sharing of data sets,
   intermediate and final results, which in turn will help multiple
   users avoiding reprocessing the same data sets.
  
 * Now getAverageFile() for AffymetrixCelSet and DChipDcpSet,
   as well as getBaseline() for ChipEffectSet drop tags from the
   output root path before creating the file.  Likewise, the target
   distribution file generated by QuantileNormalization is created
   in a root path without tags.
   Currently, this requires that aroma setting 'devel/dropRootPathTags'
   is TRUE.
  
 * Added findTargetDistributionFile() to QuantileNormalization for
   locating an existing target-distribution file.  The previously used
   getTargetDistributionPathname(), which returns a hardwired pathname,
   is now only used for creating a target-distribution file (in a
   root directory without tags).
  
 * Now convertToUnique() for AffymetrixCelSet searches for already
   available data sets using the aroma-wide search rules.  Before it
   assumed it would always be located in probeData/, but with the new
   rules it can also be in probeData,<tags>/.
  
 * ROBUSTNESS: getTimestamp() for AffymetrixCelFile no longer assumes
   that the file's DAT header contains a timestamp and tries to translate.
   Instead it first tests for the timestamp pattern, and returns NA
   if not found.
 
 
Version: 2.0.1 [2011-02-20]

 * KNOWN ISSUE: install.packages("aroma.affymetrix") does not work
   because the package depends on the 'affxparser' package which has
   to be installed from on Bioconductor.  For now, the DESCRIPTION
   file has been updated with installation instructions.
 
DEPRECATED AND DEFUNCT:

 * CLEANUP: Replaced calls to deprecated getListOfChipEffectSets()
   with getSets().
  
 
Version: 2.0.0 [2011-02-16]
  
 * No updates.  Submitted to CRAN.
 
 
Version: 1.9.5 [2011-02-15]
  
 * CLEANUP/GENERALIZATION: Now all system tests for the
   Hs_PromPR_v02 chip type use public data sets.
   Before some of them used a private data set.
   Remaining data sets that are non-public and used in system tests:
   - GenomeWideSNP_6: TCGA,OV,testSet,pairs,Broad (1 test)
  
 * HARMONIZATION: Renamed argument 'numBins' of MatNormalization
   to 'nbrOfBins'.
  
 * HARMONIZATION: Now MatNormalization utilized the aroma setting 'ram',
   which replaced argument 'numChunks' which is now deprecated.
 
 
Version: 1.9.4 [2011-02-08]
  
 * GENERALIZATION: Now it is possible to specify the range of fragment
   lengths to be considered when normalizing for PCR fragment-length
   effects.  Lengths outside the range ar treated as missing values.
   See argument 'lengthRange' to FragmentLengthNormalization.
 
 
Version: 1.9.3 [2011-02-04]
  
BUG FIXES:

 * as.character() for an empty AffymetrixCelSet would throw exception
   "Argument 'x' is of length 1 although the range ([0,0]) implies that is
   should be empty.", while trying to infer the chip type.
 
 
Version: 1.9.2 [2011-02-01]
  
 * CLEANUP/GENERALIZATION: Now all system tests for the Mapping10K_Xba142 chip
   type use public data sets. Before some of them used a private data set.
 
 
Version: 1.9.1 [2011-02-01]
  
 * GENERALIZATION: With aroma.core v1.9.3 it is now possible to
   display spatial image and write them as PNG files if the 'png'
   package is installed, alternatively to the EBImage package.
  
 * ROBUSTNESS: Removed some remaining partial argument calls.
  
 * CLEAN UP: Removed explicit dependencies on EBImage in the code.
   The dependencies are still there, but via wrapper methods of
   aroma.core.
 
 
Version: 1.9.0 [2011-01-10]
  
 * No updates.  Submitted to CRAN.
 
 
Version: 1.8.3 [2011-01-09]
  
 * Added writeCdf() for AffyGenePDInfo, which replaces pdInfo2Cdf().
   An auxillary CEL file is no longer needed to create a CDF from
   an PDInfo package.  Moreover, contrary pdInfo2Cdf(), the generated
   CDF now gets a correct/formal Affymetrix chip type.

BUG FIXES:

 * createMonocellCdf(..., verbose=FALSE) for AffymetrixCdfFile would still
   create verbose output.
 
 
Version: 1.8.2 [2010-12-04]
  
BUG FIXES:

 * Local variable 'pdName' of pdInfo2Cdf() was used before it was defined,
   which gave an error.  Thanks to Guido Hooiveld at the Wageningen
   University, Netherlands, for reporting this.
 
 
Version: 1.8.1 [2010-11-22]
  
 * ROBUSTNESS: Now extractAffyBatch() for AffymetrixCelSet asserts that
   the sample names are unique, which affy::ReadAffy() requires.
   Moreover, the sample names are now the fullnames not just the names.
 
 
Version: 1.8.0 [2010-11-07]
  
 * Committed to CRAN. No updates.
 
 
Version: 1.7.4 [2010-11-04]
  
 * ROBUSTNESS: Bumping the required versions of the dependent package
   in order to make sure we are not affected by old bugs.
 
 
Version: 1.7.3 [2010-10-02]
  
 * Now doGCRMA() automagically makes sure that the default CDF is used
   in the GcRmaBackgroundCorrection step, while use a custom CDF
   everywhere else if set.  Added argument 'type' to doGCRMA() which
   is passed to GcRmaBackgroundCorrection().
  
 * GENERALIZATION: Now GcRmaBackgroundCorrection(..., type="affinities")
   can process also chip types for which there are no MMs and for
   which non-specific probes are explicitly specified.
  
 * GENERALIZATION: Now GcRmaBackgroundCorrection calculates gcRMA probe
   affinites based on Aroma Cell Sequence (ACS) annotation files.
   For backward compatibility, it turns to Affymetrix probe-tab files
   if an ACS file is not located.
  
 * ROBUSTNESS: Added more validation of the arguments passed to
   the constructor of GcRmaBackgroundCorrection and its internal
   functions.  Also added more verbose output during processing.
  
 * CORRECTION: The DESCRIPTION file suggested a package version that
   did not exist.
 
 
Version: 1.7.2 [2010-09-06]
  
 * ROBUSTNESS: Added extractAffyBatch() for ChipEffectSet that gives
   an informative error message explaining why it doesn't make sense
   to do so.
 
 
Version: 1.7.1 [2010-08-14]
  
 * Added doGCRMA() for AffymetrixCelSet and data-set names.
   doGCRMA() runs in bounded memory and replicates the results of
   gcrma() in the gcrma package with great precision.
 
 
Version: 1.7.0 [2010-07-26]
  
 * Committed to CRAN. No updates.
 
 
Version: 1.6.8 [2010-07-21]
  
 * CLEAN UP: Now getAverageFile() for AffymetrixCelSet no longer writes
   debug information to ${Rcache}/aroma.affymetrix/idChecks/.
 
 
Version: 1.6.7 [2010-07-19]
  
 * Now byPath(..., cdf) for ChipEffectSet will silently try to retrieve
   the the monocell CDF if argument 'cdf' is the main CDF.  If it fails
   an error is thrown.  This makes it possible to specify the main/regular
   CDF (or chip type), instead of the monocell CDF, when retrieve a
   chip-effect data set.
  
BUG FIXES:

 * The above byPath(..., cdf) updated was necessary in order to be able to
   retrieve chip-effect data set byName() after the update of byName() for
   AffymetrixCelSet in the previous version.
 
 
Version: 1.6.6 [2010-07-02]
  
 * Now AffymetrixCelSet$byName(..., chipType="GenomeWideSNP_6,Full") will
   work (before chiptypes with tags would give an error).  This is now
   done by first locating the CDF for the chip type (with tags).
  
 * Added doASCRMAv1() and doASCRMAv2() for convenient allele-specific
   doCRMAv1() and doCRMAv2() wrappers.

DEPRECATED AND DEFUNCT:

 * CLEAN UP: Dropped argument 'transforms' from getImage()
   for AffymetrixCdfFile.
 
 
 
Version: 1.6.5 [2010-06-16]
  
 * Added doRMA() for AffymetrixCelSet and data-set names. doRMA() runs in
   bounded memory and replicates the results of fitPLM() in the affyPLM
   package with great precision.
 
 
Version: 1.6.4 [2010-06-07]
  
BUG FIXES:

 * Added argument shift=+300 to doCRMAv1().
 
 
Version: 1.6.3 [2010-05-30]
  
 * Now translateFullName() of AffymetrixProbeTabFile translates
   'PROBE_STRAND' to 'targetStrandedness'.
 
 
Version: 1.6.2 [2010-05-26]
  
 * Started to add scripts for downloading example data.
 
 
Version: 1.6.1 [2010-05-19]
  
 * CORRECTION: doCRMAv1() did not shift +300 the signals before
   doing the probe-level summarization.
  
BUG FIXES:

 * Fixed a bug in PdInfo2Cdf().  Thanks Kasper Daniel Hansen for the report.
 
 
Version: 1.6.0 [2010-05-14]
  
 * Package submitted to CRAN.
  
SOFTWARE QUALITY:

 * Package pass system and redundancy tests.
  
 * Package pass R CMD check on R v2.11.0 and v2.12.0 devel.
 
 
Version: 1.5.9 [2010-05-13]
  
 * SPEED UP: Now the constructor AllelicCrosstalkCalibration() is set to
   recognize the Cytogenetics_Array chip type.  This avoids having to
   scan the CDF for unit types and check for SNPs, which is slow and not
   really wanted for a constructor function.
  
 * ROBUSTNESS: Now fromDataFile() of ChipEffectFile and FirmaFile, as
   well as convertToUnique() of AffymetrixCelSet allocates/creates data
   files atomically.  As elsewhere, this is done by first creating and
   writing to a temporary file, which when complete is then renamed.
   This lowers the risk of generating incomplete files.

SOFTWARE QUALITY:

 * ROBUSTNESS: Added a redundancy test of CRMA "v1.5" for the
   Cytogenetics_Array chip type.
    
BUG FIXES:

 * convertToUnique() for AffymetrixCelSet would not recognize Windows
   Shortcut links.
 
DEPRECATED AND DEFUNCT:

 * CLEAN UP/DEPRECATED: AffymetrixCelSet$createBlankSet() was removed,
   because it has not been used anywhere since 2007.


Version: 1.5.8 [2010-05-09]
  
 * Made justSNPRMA(..., normalizeSNPsOnly="auto") for AffymetrixCelSet
   the default.
  
 * Now all findUnitsTodo() for data sets checks the data file that
   comes last in a lexicographic ordering.  This is now consistent
   with how the summarization methods update the files.  Before it
   used to be the one that is last in the data set.
  
 * Now all updateUnits() for data sets updates the data files in
   lexicographic order.
  
 * Now CrlmmModel(..., recalibrate=TRUE) is the default.
  
 * Now justSNPRMA(..., returnESet=TRUE) for AffymetrixCelSet
   returns an AlleleSet due to updates in oligo v1.12.0.
  
 * Added extractAlleleSet() to SnpChipEffectSet.  Replaces
   extractSnpQSet(), because the SnpQSet class was dropped
   in oligo v1.12.0 and replaced by the AlleleSet class.
  
BUG FIXES:

 * fit() of CrlmmModel would not work with oligo v1.12.0 and newer.
  
 * getCallSet() and getCrlmmParametersSet() of CrlmmModel used non-existing
   verbose object 'log' instead of 'verbose'.
 
 
Version: 1.5.7 [2010-04-22]
  
 * Added groupUnitsByDimension() to AffymetrixCdfFile.
  
SOFTWARE QUALITY:

 * ROBUSTNESS: Added redundancy tests for doCRMAv2() and  writeDataFrame().
  
BUG FIXES:

 * doCRMAv1() for AffymetrixCelSet used undefined 'csN' internally instead
   of 'csC'.
 
 
Version: 1.5.6 [2010-04-15]
  
BUG FIXES:

 * computeAffinities(..., verbose=FALSE) of AffymetrixCdfFile would give
   throw "Error in reset(pb) : object 'pb' not found".  Thanks Stephen ?
   at Mnemosyne BioSciences, Finland, for this report.
 
 
Version: 1.5.5 [2010-04-07]
  
SOFTWARE QUALITY:

 * ROBUSTNESS: Added a test script for gcRMA background correction
   on the MoEx-1_0-st-v1 chip type.
 
 
Version: 1.5.4 [2010-04-06]
  
 * Added an internal version of doCRMAv1().
  
 * Added argument 'plm' to existing doCRMAv2().
 
 
Version: 1.5.3 [2010-03-31]
  
 * Updated getProbeSequenceData() for AffymetrixCdfFile to recognize
   more NetAffx probe-tab files, e.g. MoEx-1_0-st-v1.probe.tab.
  
 * KNOWN ISSUES: getProbeSequenceData() for AffymetrixCdfFile requires
   that the unit names in the probe-tab file match the ones in the
   CDF.  This may cause issues if custom CDFs with custom unit names
   are used.  This is another reason why we should move away from
   probe-tab files and instead use aroma binary cell sequence files.
 
 
Version: 1.5.2 [2010-03-26]
  
 * Added argument 'defValue' to createFrom() for AffymetrixCelFile
   so that one can specify the default value for cleared elements.
 
 
Version: 1.5.1 [2010-03-14]
  
BUG FIXES:

 * allocateFromCdf() of AromaCellCpgFile, AromaCellPositionFile, and
   AromaCellMatchScoreFile would drop all but the first tag.
 
 
Version: 1.5.0 [2010-02-22]
  
 * Submitted to CRAN.  No changes since v1.4.9.
  
SOFTWARE QUALITY:

 * Package passes all redundancy tests.
 
 * Package passes R CMD check on R v2.10.1 patch and R v2.11.0 devel.
  
 
Version: 1.4.9 [2010-02-22]
  
 * Added AromaCellCpgFile.
  
SOFTWARE QUALITY:

 * Added test script for AromaCellCpgFile and AromaCellPostionFile.
  
BUG FIXES:

 * The settings in 'aromaSettings' loaded by aroma.core was overridden by
   default settings of aroma.affymetrix, even if they already existed.
 
 
Version: 1.4.8 [2010-02-21]
  
 * ROBUSTNESS: Now updateUnits() of ChipEffectSet updates the files in
   lexicographic order.  Before there was a risk that this was not done
   if fullname translators are changing the lexicographic ordering.
  
 * MEMORY OPTIMIZATION: Now updateUnits() of ChipEffectSet cleans out the
   temporary data object extracted for each chip-effect file written.
   It also calls the garbage collector after each file written.
  
 * Added verbose output to updateUnits() of ProbeAffinityFile.
 
 
Version: 1.4.7 [2010-02-16]
  
 * MEMORY OPTIMIZATION: Now process() of AllelicCrosstalkCalibration
   clears the in-memory cache when finished.
  
 * MEMORY OPTIMIZATION: Now AbstractProbeSequenceNormalization classes
   cleans out more unneeded objects.
  
 * MEMORY OPTIMIZATION: Now doCRMAv2() removes as much as possible.
  
BUG FIXES:

 * readDataUnitChromosomePosition() of AffymetrixNetAffxCsvFile failed to map
   chromosome 'MT' to 25.  This bug was introduced in aroma.affymetrix v1.0.7.
 
 
Version: 1.4.6 [2010-02-13]
  
 * Added an internal version of doCRMAv2().
  
BUG FIXES:

 * exportTotalAndFracB() of SnpChipEffectSet returned all arrays in the output
   data set directory and not only the ones part of the input data set.
 
 
Version: 1.4.5 [2010-02-10]
  
SOFTWARE QUALITY:

 * Added redundancy test for calculating bias-corrected sex-chromosome
   copy numbers.
 
 
Version: 1.4.4 [2010-02-08]
  
 * Added appendVarArgs(boxplot.stats) so that one can pass argument
   'show.names' to bxp() via plotRle().
 
 
Version: 1.4.3 [2010-02-03]
  
SOFTWARE QUALITY:

 * Package passes R CMD check and all redundancy tests.
 
 
Version: 1.4.2 [2010-02-02]
  
 * Updated to work with R.filesets v0.7.4 and aroma.core v1.4.4.
 
 
Version: 1.4.1 [2010-01-06]
  
 * Now all binary files allocated have default NA values.  This is done
   by an update in aroma.core v1.4.1.
 
 
Version: 1.4.0 [2010-01-04]
  
SOFTWARE QUALITY:

 * Package passes R CMD check on R v2.10.1 and R v2.11.0 devel and
   all of its redundancy tests.
 
BUG FIXES:

 * After loading aroma.affymetrix, findCdf() would give "Error in if
   (regexpr(pattern, chipType) != -1) { : argument is of length zero",
   because AffymetrixCdfFile$findByChipType(chipType=NULL) was not valid.
   Now the latter returns NULL without complaining.
  
 
Version: 1.3.6 [2010-01-02]
  
 * Adopted to work with aroma.core v1.3.7 and R.filesets 0.7.0.
  
 * ROBUSTNESS: Using new Arguments$getInstanceOf() were possible.
  
 * ROBUSTNESS: Now all index arguments are validated correctly
   using the new 'max' argument of Arguments$getIndices().  Before
   the case where "max == 0" was not handled correctly.
 
 
Version: 1.3.5 [2009-12-04]
  
BUG FIXES:

 * The test for allowing ASCII CDFs or not in setCdf() of an AffymetrixCelSet
   was only applied if getOption(aromaSettings, "rules/allowAsciiCdfs") was
   TRUE (should be FALSE).
 
 
Version: 1.3.4 [2009-11-24]
  
 * CLEAN UP: Removed packages GLAD, DNAcopy and HaarSeg from the
   list of suggested packages in DESCRIPTION.
  
 * CLEAN UP: Move more method for 'profileCGH' objects to aroma.core.
 
 
Version: 1.3.3 [2009-11-19]

DEPRECATED AND DEFUNCT:

 * CLEAN UP: Move all (generalized) ChromosomalModel,
   CopyNumberChromosomalModel, and CopyNumberSegmentationModel
   to aroma.core from here.
 
 
Version: 1.3.2 [2009-11-18]
  
 * GENERALIZATION: Removed all dependencies on Affymetrix data types
   for ChromosomalModel, CopyNumberChromosomalModel, and
   CopyNumberSegmentationModel.
  
 * Added internal getNumberOfFilesAveraged() to CnChipEffectFile.
  
 * Added isAverageFile() for AffymetrixCelFile.
  
 * Added CnChipEffectSetTuple extending ChipEffectSetTuple.
  
 * Now getChromosomes() of ChromosomalModel utilized UGP files (only).
   DChip GenomeInformation files are no longer supported.
 
 
Version: 1.3.1 [2009-11-13]
  
 * ROBUSTNESS: Now arguments 'ces' and 'ref' and CopyNumberChromosomalModel
   have to be CnChipEffectFile|Set, otherwise an exception is thrown.
   Before it was possible to pass a SnpChipEffectSet unnoticed, although
   only total CNs are modelled.  Added a test to testScripts/robustness/
   asserting this.  Thanks Pierre Neuvial at UC Berkeley for this report.

DEPRECATED AND DEFUNCT:

 * CLEAN UP: Moved most of AromaUflFile to aroma.core (from aroma.affymetrix).
 
 
Version: 1.3.0 [2009-11-01]
  
 * New public release.
  
 * More recent dependencies on Bioconductor packages.
  
SOFTWARE QUALITY:

 * Package passes R CMD check on R v2.10.0 and all redundancy tests.
 
 
Version: 1.2.3 [2009-10-26]
  
 * Added getExtensionPattern() to those GenericDataFile classes that
   have "single" filename extension, e.g. *.cfh but not *.cdf.bin.
   The other will be incorporated when we have thoroughly gone through
   the impact of including those as well.

BUG FIXES:

 * Fitting RlmPlm() would give an error reporting on a call to an internal
   preprocessCore function is incompatible.  This occured with
   preprocessCore v1.7.1 or newer.

 
Version: 1.2.2 [2009-10-16]
  
 * CLEAN UP: Cleaned up dependencies in DESCRIPTION.
 
 
Version: 1.2.1 [2009-10-02]
  
 * Added argument 'onDuplicates' to importFromAffymetrixProbeTabFile() for
   AromaCellSequenceFile.  If "error" ("warning"), an exception (warning)
   is generated whenever duplicated cell indices are detected in the probe
   tab file.  If "ignore", they are ignored, which means that the last
   duplicated probe sequence will be what is finally imported.
  
 * Added argument 'keepSequenceLengths' to importFromAffymetrixProbeTabFile()
   for AromaCellSequenceFile so that one can drop sequences of incorrect
   lengths, cf. HuGene-1_0-st-v1.probe.tab.
  
 * Added getDefaultFullName() to AffymetrixFileSet and CnagCfhSet.
  
 * CLEAN UP: Updated to use byPath() instead fromFiles().
  
BUG FIXES:

 * Now getCdf() for AffymetrixProbeTabFile first searches for a CDF with
   filename <chipType>.cdf, then <chipType>,.*.cdf.
 
DEPRECATED AND DEFUNCT:

 * CLEAN UP: Removed all getFullName() for all GenericDatFileSet classes.


Version: 1.2.0 [2009-09-09]
  
 * New public release.
  
SOFTWARE QUALITY:

 * Package passes R CMD check on R v2.9.2 and all redundancy tests.

BUG FIXES:

 * Fixed broken/missing Rd links.
  
 
Version: 1.1.5 [2009-09-07]
  
DEPRECATED AND DEFUNCT:

 * Renamed getUnitsOnChromosome() to getUnitsOnChromosomes() for the
   GenomeInformation class.  The former now calls the latter for backward
   compatibility.  This was done to make it more consistent with a
   similar method in aroma.core.
 
 
Version: 1.1.4 [2009-09-05]
  
 * CLEAN UP: Removed the geneplotter package from Suggests:.
  
BUG FIXES:

 * A few plot functions would generate "Error: 'smoothScatter' is not an
   exported object from 'namespace:geneplotter'".  This would occur with
   geneplotter v1.21.5 or newer.  This is because we called
   geneplotter::smoothScatter(), but that function was moved from
   geneplotter v1.21.4 to the graphics package of R v2.9.0.  For backward
   compatibility, we now provide a patch (in aroma.core).

DEPRECATED AND DEFUNCT:

 * CLEAN UP: Now static methods fromChipType() and fromName() of
   AffymetrixCelSet and other classes are defunct.  Instead, use static
   methods byChipType() and byName() instead.
 
 
Version: 1.1.3 [2009-08-12]
  
 * Now findByName() of AffymetrixCnChpSet, CnagCfhSet, and DChipDcpSet also
   utilize ditto of AffymetrixCelSet, because the code was identical to the
   latter.
  
 * Now findByName() of AffymetrixCelSet calls ditto of GenericDataFileSet of
   the R.filesets packages, which means that Windows Shortcut links also in
   subdirectories are recognized.
 
 
Version: 1.1.2 [2009-07-08]
  
 * Added getListOfUnitTypesFiles() to AffymetrixCelSetTuple,
   ArrayExplorer, and ChromosomalModel.
  
 * Added getUnitTypesFile() for AffymetrixCdfFile, AffymetrixCel{File|Set},
   AffymetrixCnChpFile, AffymetrixPlatform and TransformReport.
  
 * Now AffymetrixCdfFile implements also the UnitTypesFile interface.
  
 * ROBUSTNESS: Updated process() of AbstractProbeSequenceNormalization to
   write to a temporary file which is the renamed.  This will lower the
   risk for generating corrupt files in case of interrupts.
 
 
Version: 1.1.1 [2009-06-30]
  
 * Moved packages 'gcrma' and 'gsmoothr' from "Imports:" to "Suggests:",
   because the former class of packages is required by R CMD check,
   whereas the latter is not (via an option).  This will allow the
   package to build and pass the checks on the CRAN servers.

BUG FIXES:

 * Added missing getExpectedOutputFullnames() for MatSmoothing.

 * ROBUSTNESS/BUG FIX: Now plot() of CopyNumberSegmentationModel asserts
   that the RColorBrewer package is available at the very beginning.  This
   will avoid generating image files where the data points are missing.
  
 
Version: 1.1.0 [2009-05-29]
  
 * New public release. No updates.
  
SOFTWARE QUALITY:

 * Package passes R CMD check on R v2.9.0 and all redundancy tests.
 
 
Version: 1.0.8 [2009-05-27]
  
 * SPEED UP: Now process() of MatSmoothing is several times faster
   due to code optimization and utilizing of the new 'gsmoothr' package.
  
 * ROBUSTNESS: Updated process() of MatSmoothing to write first to
   a temporary file which is then renamed.  This lower the risk for
   corrupt output files due to processing interrupts.
  
 * ROBUSTNESS: Now the constructor of MatSmoothing does more tests
   of the validity of the 'design' matrix argument.
  
 * Now the chip type validation of fromFiles() for AffymetrixCelSet
   is aware of tags in the chip type of the CEL files. This may happen
   if custom CDFs are used are their full chip types are stored in the
   CEL files, e.g. Hs_PromPR_v02,Harvard,ROIs,unique.
 
 
Version: 1.0.7 [2009-05-20]
  
 * Now readDataUnitChromosomePosition() for AffymetrixNetAffxCsvFile
   also recognize 'M' for chromosome 25.
  
 * GENERALIZATION: Updated fitCnProbes() of UnitModel to identify
   single-cell CN units, and ignore multi-cell CN units, which will
   be process like the other units.  By not assuming single-cell CN
   units, this methods should also apply to other CDFs, e.g. the
   new Cytogenetics_Array.
  
 * CLEAN UP: Moved the Explorer class and its support files under
   inst/ from aroma.affymetrixd to aroma.core.
  
 * CLEAN UP: Moved the AromaCellPositionFile class from
   aroma.affymetrix to aroma.core.
 * EXCEPTION HANDLING: Methods that creates/modifies files will give
   a clear error message if the file permissions does not allow it.
  
 * ROBUSTNESS: Now all arguments that are expected to be exactly one
   character string (not an empty vector or a vector of length two)
   are asserted to be that too.  This closes some potential bugs.
  
 * Package passes R CMD check on R v2.9.0.

BUG FIXES:

 * getCdf() for AffymetrixProbeTabFile would fail if the CDF had no tags.
  
 * fit() for CrlmmModel was calling oligo::getM(), but that method was later
   moved to oligoClasses.  Now we just do getM().

DEPRECATED AND DEFUNCT:
  
 * Removed obsolete patch of affxparser cdfMergeStrands().
  

 
Version: 1.0.6 [2009-05-16]

 * CLEAN UP: Generalized CopyNumberSegmentationModel such that
   subclasses no longer have to implement fitOne(), but instead
   only getFitFunction(), which should return a segmentByNnn()
   function for the RawCopyNumbers class.
  
 * CLEAN UP: Moved all drawCnLevels(), extractCopyNumberRegions()
   and extractRawCopyNumbers() [for DNAcopy, HaarSeg and profileCGH]
   to aroma.core v1.0.6 (will eventually end up in aroma.cn).

BUG FIXES:

 * In the most recent version of oligo, its justSNPRMA() requires that oligo
   is loaded, i.e. oligo::justSNPRMA() will not work.  Updated justSNPRMA()
   for character to require oligo.
  
DEPRECATED AND DEFUNCT:
  
 * CLEAN UP: Removed obsolete fitGlad() for CnChipEffect{File|Set}.
 
 
Version: 1.0.5 [2009-05-10]
  
 * BETA: Updated several methods of the package to handle the new
   way getOutputDataSet() of AromaTransform scans and loads
   data sets.  This new way is the first step towards supporting
   output directories that contains more data files than the
   input data set, which for instance can occur if the same
   data set is split up and processed in subsets.  The new
   approach will also try to order the output files accordingly
   with the input files.
  
 * Added readSequenceDataFrame() for AffymetrixProbeTabFile.
  
 * Updated getFitUnitGroupFunction() of RmaPlm to work with the
   new oligo v1.7.19 as well.
  
 * CLEAN UP: computeAffinities() of AffymetrixCdfFile loaded the
   'matchprobes' package, but never used it.
  
 * CLEAN UP: Now computeAffinities() of AffymetrixCdfFile uses
   the AffymetrixProbeTabFile class to read probe sequences.
  
 * CLEAN UP: Now findByChipType() of AffymetrixProbeTabFile only
   search according to "modern" rules.  The by now really old
   alternative search rules have been made deprecated, i.e. it
   still uses those but, if a file is found, it gives an error
   saying that the the method is outdated.  This should not
   affect anyone these days, but just in case, it is included.
  
SOFTWARE QUALITY:

 * Package passes redundancy tests.

 * Package passes R CMD check on R v2.9.0.
  

 
Version: 1.0.4 [2009-04-16]
  
 * BETA: Added NormExpBackgroundCorrection which does background
   correction according to the normal exponential model. It
   utilizes the limma package for this. The default settings give
   identical results as RmaBackgroundCorrection, which uses affy.
  
 * Made several modifications to computeAffinities() for
   AffymetrixCdfFile which allows us to compute affinities also
   for PM-only chip types, e.g. Gene 1.0 ST arrays: (i) added a
   different stream for PM-only (with NCs), (ii) left the PM+MM
   array code mostly untouched, and (iii) fixed some assumptions
   about the columns of the probe_tab file.

BUG FIXES:

 * The GcRmaBackgroundCorrection method would mix up PMs and MMs in the model
   estimation. This bug was introduced in aroma.affymetrix v0.3.4 (January 20,
   2007). It was located to the internal bgAdjustGcrma() method.
 
 
Version: 1.0.3 [2009-03-22]
  
 * BETA: Added GcContentNormalization2 which extends the generic
   AdditiveCovariateNormalization class.
  
 * BETA: Added abstract AdditiveCovariateNormalization.
  
 * BETA: Added AromaUnitGcContentFile and AromaUgcFile to hold GC contents.
 
 
Version: 1.0.2 [2009-02-22]
  
 * Added getCdfBin() and getChipType() to DChipDcpSet.
  
 * Added findByChipType() and byChipType() to DChipCdfBinFile.
   Added argument fullname=TRUE to getChipType() of DChipCdfBinFile.
  
 * Added exportTotalCnRatioSet() to AffymetrixCnChpSet.
  
 * Wherever argument 'ram' exists, it defaults to the value of a
   global settings.  To change the default, do for instance
   setRam(aroma.affymetrix, 10).
  
 * CLEAN UP: Removed the implementation of byChipType() for the
   AromaUnitTabularBinaryFile class that would scan annotationData/
   for matching CDFs before deciding which file to use.  That class
   should not depend on a specific platform.  Now the implementation
   is solely in the aroma.core package.

DEPRECATED AND DEFUNCT:
  
 * CLEAN UP: Removed deprecated argument 'moreUnits' of fit() of
   ProbeLevelModel.  Use argument 'ram' instead.
 
 
Version: 1.0.1 [2009-02-13]
  
 * Added getAromaUnit{Total|FracB}CnFileSet() to SnpChipEffectSet, which
   uses protected exportTotalAndFracB() to SnpChipEffect{File|Set}.
  
 * ROBUSTNESS: Added support for optional validation/selection by the
   number of units/cells to all static byChipType() methods.  This is
   done by specifying argument nbrOfUnits/nbrOfCells.
  
 * CLEAN UP: Suppressing warnings about "truncating string with
   embedded nul" in rawToChar() when using affxparser::readCcgHeader().
  
 * CLEAN UP: Cleaned up the MatSmoothing class.
  
 * CLEAN UP: Cleaned up the AffymetrixCelSetTuple class.

SOFTWARE QUALITY:

 * Package pass R CMD check and all redundancy tests.

BUG FIXES:
  
 * setMergeStrands() of SnpPlm and setCombineAlleles() of CnPlm did not update
   the setting of the PLM itself, only the settings of the underlying
   parameter files.  SnpPlm itself, only only the underlying parameter files.
   Added getMergeStrands() to SnpPlm and getCombineAlleles() to CnPlm.
 
 
Version: 1.0.0 [2009-01-12]
  
 * Added alpha version of the CrlmmModel (currently only for 100K & 500K).
  
 * Added justSNPRMA() replicating ditto in the oligo package.
  
 * Added alpha version of the HaarSegModel.
  
 * Added plotAllelePairs() for AllelicCrosstalkCalibration.
  
 * Added argument 'zooms' to the constructor of ChromosomeExplorer.
  
 * Now process() of AlleleSummation returns immediately if already done.
  
 * Added more methods and classes which eventually will allow
   analysis of Affymetrix tiling arrays.
  
 * Added trial version of AromaCellPositionFile.
  
 * Added extractCNT() and writeCNT() for SnpChipEffect{File|Set}, which
   exports CNT data files that can be imported by Affymetrix GTC Browser.
  
 * Added argument 'units' to readDataFrame() to GenomeInformation.
  
 * ROBUSTNESS: Now MultiArrayUnitModel:s assert that there are at least
   two arrays in the data set.
  
BUG FIXES:
  
 * CLEAN UP: createFrom() for AffymetrixCelFile had verbose=TRUE as default.
  
 * AlleleSummation would not work for chip types containing exclusively SNP
   units.  It expected some non-SNP units.
  
 * There was no extractTotalAndFreqB() for CnChipEffectSet, but only for
   CnChipEffecSet (misspelled). Thanks Pierre Neuvial for spotting this.
  
 * Now process() avoids sets of pairs with too few probe pairs. This could
   happen because of the new getSetsOfProbes() working off the probe sequence
   files.
  
 * getUnitIntensities() of AffymetrixCelSet would drop the array dimension if
   only one array was read.  This caused for instance PLM fitting to given an
   error when only one array was included.
  
 * Methods returning ChipEffectSet would not "update" the returned data set,
   which for instance had the effect of not updating/setting attributes for
   sample annotation files.
  
 * Lines of code (excluding comments) using grep -v "#" *.R | wc -l:
   aroma.affymetrix + aroma.core: 43657+10510 = 54167.
 
 
Version: 0.9.6 [2008-12-04]
  
 * Now CbsModel and GlabModel display any optional/additional
   arguments passed to the internal segmentation method in
   the verbose output.
  
 * Added argument 'model' for AllelicCrosstalkCalibration to quickly
   specification of default parameter settings according to the CRMA and
   CRMA v2 model.
  
 * Added argument 'pairBy' for AllelicCrosstalkCalibration to specify
   how the allele probe pairs are identified.  Historically we inferred
   this from the CDF, but it is safer and more generic to do this from
   the probe sequences, which then requires an ACS annotation file.
  
 * Now argument 'targetFunctions' of FragmentLengthNormalization can also
   be "zero", which then specifies a predefined constant target function.
  
 * Added support for importing probe sequences from Affymetrix BPMAP files
   via the importFromBpMap() for AromaCellSequenceFile.
  
 * Added classes and methods in preparation for supporting analysis
   of tiling arrays.
  
 * Now fitCnProbes() of UnitModel only fits non-fitted CN units.
  
 * SPEED UP: extractMatrix() of AffymetrixCel{File|Set} is now faster
   when argument 'cells' is specified.
  
 * SPEED UP: Now BasePositionNormalization is 2-3 times faster
   due to memoization and a more clever prediction algorithm.
  
 * MEMORY OPTIMIZATION: Added abstract normalization class
   LinearModelProbeSequenceNormalization that fits linear models
   based on probe sequences in bounded memory.  This is done by
   building up the normal equations incrementally and then call
   solve().  It is the generation of normal equations that otherwise
   consume most of the memory.  The BasePositionNormalization
   class now inherits from this memory-efficient class, which
   means we can now do probe-position normalization on GenomeWideSNP_6
   arrays using less than 1GB of RAM.
  
 * MEMORY OPTIMIZATION: Forgot to clean out weight estimates in
   ProbeLevelModel objects when cleaning out the memory cache.

BUG FIXES:
  
 * For allele-specific estimates, FragmentLengthNormalization would correctly
   estimate normalization scale factors, but due to a typo, it effectively
   only update the signals for allele A.  According to the source code
   repository, this has been a bug from the very beginning
   when allele-specific estimates was claimed to be supported.
  
 * RmaPlm(..., flavor="oligo") was broken, because oligo was updated.
 
 
Version: 0.9.5 [2008-10-17]
  
 * Package pass R CMD check on R v2.7.2 and R v2.8.0rc.
 
 
Version: 0.9.4.7 [2008-10-16]
  
 * Added nbrOfCellsPerUnitGroup() and nbrOfCellsPerUnit() for
   AffymetrixCdfFile.

DEPRECATED AND DEFUNCT:
  
 * Renamed getFitFunction() for all PLMs to getFitUnitGroupFunction(),
   because the latter is much more explanatory.
 
 
Version: 0.9.4.6 [2008-09-19]
  
BUG FIXES:
  
 * process() of FragmentLengthNormalization did not return a data set for
   which the sample attributes has been updated according to optional sample
   annotation files (SAFs).
 
 
Version: 0.9.4.5 [2008-09-17]
  
 * Added argument 'onMissing' to FragmentLengthNormalization, which is
   passed down to normalizeFragmentLength() [req aroma.light v1.9.2] to
   make it possible to normalize also units for which fragment lenghts
   are unknown.  Previously such units were not normalized - for
   backward compatibility, onMissing="ignore" does exactly that.
  
 * Now it is possible to specify enzyme names in argument 'enzymes' to
   readDataUnitFragmentLength() of AffymetrixNetAffxCsvFile.
  
 * Added argument 'enzymesToUpdate' to importFromAffymetrixNetAffxCsvFile()
   of AromaUflFile in order to make it possible to specify both which
   enzymes to read and to update.
  
 * ANNOTATION: Updated  annotationData/genomes/Human,chromosomes.txt
   to contain data for the Mitochondrial genome ("chromosome") as well.
  
 * CONSISTENCY: Now argument 'subset' of plotDensity() of AffymetrixCelFile
   and AffymetrixCelSet defaults to NULL (all probes).  Before it was
   specifying the fraction 1/2 by default.
  
 * DEPENDENCIES: Now aroma.affymetrix requires affxparser 1.13.8,
   because getUnitTypes() of AffymetrixCdfFile requires that version
   in order to correctly identify copy-number units.
  
 * CLEANUP: Moved the handling of 'probeModel' and 'shift' to
   UnitModel from ProbeLevelModel.
  
BUG FIXES:
  
 * TYPO: The error message for argument 'dataSet' in UnitModel() returned
   multiple strings, one per class.
 
 
Version: 0.9.4.3 [2008-08-30]
  
 * Added options 'mergeStrands' and 'B' to AllelicCrosstalkCalibration.
  
BUG FIXES:
  
 * Now the affy, affyPLM, and EBImage packages are forced to be after all of
   aroma.affymetrix, aroma.light, and R.huge on the search() path.
 
 
Version: 0.9.4.2 [2008-08-23]
  
 * Moved the functions for reading dChip files to the new dChipIO package.
  
 * Now readDataUnitChromosomePosition() of AffymetrixNetAffxCsvFile also
   recognizes chromosome "MT" (mitochondrial).  It is encoded as Chr25.
  
 * BETA: Added class AffymetrixCnChpSet.
 
 
Version: 0.9.4.1 [2008-08-19]
  
 * Added argument 'arrays' to process() of ArrayExplorer so that it is
   possible to specify for which arrays images should be generated.
  
 * Added support for specifying the type of target effects for any
   AbstractProbeSequenceNormalization method.
  
 * ALPHA: Added argument 'flavor' to AllelicCrosstalkCalibration. However,
   fitGenotypeCone() of aroma.core has to be updated to recognize it.
  
 * ALPHA: Added ReseqCrosstalkCalibration.
 
 
Version: 0.9.4 [2008-08-02]
  
 * Public release.

SOFTWARE QUALITY:

 * Package passes R CMD check on R v2.7.1 and R v2.8.0 devel on WinXP.
 
 * Package passes all redundancy tests without errors.
 
 
Version: 0.9.3.5 [2008-07-31]
  
 * UPDATE: Now computeAffinities() for AffymetrixCdfFile gives an error
   if there are no MMs in the CDF.
  
BUG FIXES:
  
 * computeAffinities() for AffymetrixCdfFile searched for the probe-tab file
   using the chip type given by the fullname of the CDF and not the basic
   name.
 
 
Version: 0.9.3.4 [2008-07-30]
  
 * Now getGenomeInformation() and getSnpInformation() reports the reason
   for why it thinks the located object is incompatible with the CDF.
  
 * MEMORY OPTIMIZATION: Now argument 'ram' is passed down to
   getChipEffectSet() which in turn pass it down to getMonocellCdf(),
   which pass it to createMonocellCdf() in case the monocell CDF is
   missing.  This increases the chances that fit(..., ram=<small value>)
   will work with small amount of RAM.
  
 * MEMORY OPTIMIZATION: Now the validation part of createMonocellCdf()
   for AffymetrixCdfFile is also sensitive to the 'ram' argument.
 
 
Version: 0.9.3.3 [2008-07-22]
  
 * MEMORY OPTIMIZATION: Pre-allocation of matrixes that start off with
   all NAs was always done by matrix(NA, ...), but since 'NA' has mode
   "logical" this would mean that non-logical matrixes would be coerced
   as soon as they were assigned as value.  Updated all pre-allocation
   to be done as matrix(naValue, ...) where 'naValue' is of the correct
   storage mode.
  
 * Now all findByName() assert that the data set name is not empty.

 * CLEANUP: Removed allocateFromCdf() specific to AromaUgpFile since
   that is now implemented in a super class.

 * ALPHA: Added BasePositionNormalization.
 
BUG FIXES:
  
 * getAromaCellSequenceFile() of BaseCountNormalization would search using the
   full name of the chip type, e.g. GenomeWideSNP_6,Full.
  
 * byChipType() of AromaUnitTabularBinaryFile failed to locate a valid tabular
   file if more than one was found and it was not the last one that was
   matching.
  
 
Version: 0.9.3.2 [2008-07-16]
  
 * Now AffymetrixProbeTabFile inherits from TabularTextFile and
   "implements" AromaPlatformInterface.  Previously it inherited
   from the AffymetrixFile class.
  
 * Added extractMatrix() to AffymetrixCelFile for completeness.
  
 * Added argument 'drop=FALSE' to all extractMatrix(), extractTheta(),
   and extractTotalAndFreqB().
  
 * Added support for specifying the reference of any
   CopyNumberChromosomalModel as a single file (or a list of files
   if more than one set is used).
  
 * MEMORY OPTIMIZATION: When calling extractRawCopyNumbers(obj) on an
   CopyNumberChromosomalModel object, the result would be cached in memory
   (in the object). This would result in an increasing memory usage when
   data was extracted from more and more arrays. The cache could be cleared
   by calling gc(obj), but avoid this problem by default, the method does
   no longer cache results.  To cache, the method has to be called with
   argument 'cache=TRUE'.  Thanks Jason Li for reporting this.
 * BETA: Added BaseCountNormalization.
  
 * BETA: Updated FragmentLengthNormalization to handle allele-specific
   chip effect estimates as well.
  
 * Lines of code (excluding comments) using grep -v "#" *.R | wc -l:
   aroma.affymetrix + aroma.core: 24902+8638=33540.

BUG FIXES:
  
 * extractMatrix() of AffymetrixCelSet returned cells in a different than
   requested.  Thanks Mark Robinson for reporting this.
  
 * getChipType() of AffymetrixCelFile did not pass down '...' causing for
   instance getChipType(..., fullname=FALSE) to still return tags for
   ChipEffectFile:s.
  
 * plm$treatNAsAs == "NA" for RmaPlm:s returned an incorrect number of probe
   affinities whenever missing values were exluded.
  

Version: 0.9.3 [2008-06-08]
  
SOFTWARE QUALITY:

 * Package passes R CMD check on R v2.7.0 patched. There are some
   warnings of broken links in the Rd pages though.
  
 * Package passes all redundancy tests (processing time 17h 30min).
 
 
Version: 0.9.2.6 [2008-06-07]
  
 * Update filename pattern for getOutputFiles() of Transform.
  
 * Added missing getParameterSet() to ExonRmaPlm, so that 'mergeGroups'
   is also returned.

 * BETA: Added setParallelSafe() to Explorer classes to make them (somewhat)
   resistant against race conditions occuring when you run them on the
   same data set in parallel.

BUG FIXES:
  
 * readUnits() would throw 'Error in readCelUnits(pathnames, cdf
   = cdf, ...) : No CDF file for chip type found: GenomeWideSNP_6', if
   the CDF was set to GenomeWideSNP_6,Full.CDF and no GenomeWideSNP_6.cdf
   file was found.  This was because readUnits() retrieve (x,y) information
   units, which requires affxparser::readCelUnits() to locate the CDF to
   infer the number of probe column in order to map (x,y) to cell indices.
   Now readUnits() get the cell indices directly using getCellIndices().
   Thanks Yue Hu for noticing this problem.
  
 * The validation of arguments 'ceList' and 'refList' to internal
   getRawCnData() of CopyNumberChromosomalModel was too conservative. This
   caused it to throw 'Exception: Argument 'ceList' contains a non-
   ChipEffectFile: NULL' whenever multiple ChipEffectSet:s were modelled
   and one of them did not have data for one sample.  One of the redundancy
   tests for the 100K platform was updated to test for this scenario.
   Thanks to Lavinia Gordon for spotting this.
  
 * If no reference sets has been specified, then
   getReferenceSetTuple() of CopyNumberChromosomalModel would
   return too few reference files if some arrays were misssing for
   certain chip types. Thanks to Lavinia Gordon for spotting this.
  
 * updateOnLoadJS() of ArrayExplorer did not use the fullname
   chip type, cause an error in ArrayExplorer:s for tagged chip types.
   Thanks to Maria Traka at BBSRC in UK for spotting this.

 
Version: 0.9.2.5 [2008-05-28]
  
 * Cleaned up a bit.  Package now pass R CMD check.
 
 
Version: 0.9.2.4 [2008-05-25]
  
 * All extracted RawCopyNumbers objects now also set the 'chromosome' field.
  
 * Now Transform inherits from new generic aroma.core::AromaTransform.
 
 
Version: 0.9.2.3 [2008-05-21]
  
 * CLEAN UP: Moved more classes and methods from aroma.affymetrix to
   aroma.core: RawCopyNumbers, CopyNumberRegions, CopyNumberOutliers.
   Moved attribute methods from AffymetrixCel{File|Set} to
   AromaMicroarrayDataSet.  Moved stextNnn() methods from AffymetrixFile
   to AffymetrixMicroarrayDataSet.
   Created superclass AromaMicroarrayDataSetTuple of AffymetrixCelSetTuple.
   There is probably more that was moved to aroma.core that I forgot
   to mention here.  Please see aroma.core NEWS as well.
  
SOFTWARE QUALITY:

 * Package passes R CMD check on R v2.7.0 patched. There are some
   warnings of broken links in the Rd pages though.
  
 * Package passes all redundancy tests.
 
 
Version: 0.9.2.2 [2008-05-16]
  
 * Now NnnChipEffectSet parameters are by default set by the
   parameters of the first file.
  
 * Added support for getFullNames(..., translate=TRUE)
   of AffymetrixCelSetTuple.
 
 
Version: 0.9.2.1 [2008-05-11]
  
 * Added allocate() to AromaUgpFile.
 
 
Version: 0.9.2 [2008-05-10]
  
 * MAJOR: Moved all methods and classes that are independent of
   platform (e.g. GenericDataFile) to a new package aroma.core.

 * ALPHA: Inserted new classes AromaMicroarrayData{File|Set} and
   AromaChipTypeAnnotationFile into the class hierarchy.

SOFTWARE QUALITY:

 * Package passes all redundancy tests (which takes approx 24
   hours to run) on R v2.6.1 on Linux.
 
 
Version: 0.9.1.4 [2008-05-09] (Never released)
  
 * Added byName() to AffymetrixCdfFile, which is identical to byChipType().
  
 * Added argument 'rows' to readDataFrame() for GenericTabularFile.
  
 * SPEEDUP: The internal getUnitGroupNamesFromUgcMap() for AffymetrixCdfFile
   was painfully slow for large UGC maps. Instead of 10-15 days(!) for
   for GenomeWideSNP_6, it now takes 50 seconds.  This speeds up
   extractDataFrame(..., addNames=TRUE) for ChipEffectSet:s substantially.
   Thanks Nicolas Stransky for reporting this.
  
 * UPDATE: Updated readDataUnitFragmentLength() of AffymetrixNetAffxCsvFile
   to support the NetAffx r25 CSV files.
  
 * UPDATE: Now generic attributes are handled by GenericDataFile.
  
 * CONSISTENCY: Now the FirmaModel also has calculateResidualSet() just
   as ProbeLevelModel got it.
  
 * CONSISTENCY: Renamed argument 'chromosome' of getUnitsAt() of
   AromaUgpFile to 'chromosomes'.  This was done in order to make it
   consistent with getUnitsOnChromosome() of GenomeInformation. Thanks
   Tim Keighley at CSIRO for pointing this out.
  
 * CLEAN UP: Package R.native is no longer suggested.
  
 * CLEAN UP: Moved several methods to new package 'matrixStats' that is
   specialized and optimized for matrix operations.
  
 * CLEAN UP: Moved normalizeQuantileSpline(), normalizeFragmentLength,
   plotXYCurve, and predict() for lowess to aroma.light v1.7.2.
  
 * CLEAN UP: Removed "patches" for rowMedians() and as.<basic data type>()
   since they are now available in all R v2.6.x installations.
  
 * CLEAN UP: Renamed all readData() methods that return a data.frame
   to readDataFrame().
  
 * CLEAN UP: Now we're using construct foo(static, ...) instead of
   static$foo(...) internally.
  
 * ALPHA: Added getImage() for AromaUnitTabularBinaryFile and
   AffymetrixCdfFile.
  
 * ALPHA: Added writeColumnsToFiles() for GenericTabularFile.
  
 * ALPHA: By using process(..., aliased=TRUE) for ChromosomeExplorer
   the names of generated PNG files are inferred from the aliased
   full names.  This makes it possible to control the names of across
   multiple chip types without having to rename the files.  Note,
   aliased=TRUE is currently only working to alias the tags, whereas
   any aliased name portions are still ignored.

BUG FIXES:

 * readRawData() for AffymetrixCelFile did not handle a zero-length 'indices'
   argument; it was interpreted as NULL, i.e. read everything.  This is
   actually a bug in affxparser.
  
 * getUnitGroupCellMap() for ChipEffectFile, ResidualFile, WeightsFile, and
   FirmaFile, gave an error if argument 'units' had zero length (non-NULL).
  
 * Now it is possible to pass argument 'paths' to byName() of
   AffymetrixCelSet, which in turn pass it to findByName().
  
 * getChipType(..., fullname=FALSE) of AffymetrixCdfFile would return the chip
   type as the 'tags' attribute if there were no tags.
  
 * The default drawExtraAnnotations() returned error <simpleError in
   UseMethod("estimateStandardDeviation"): no applicable method for
   "estimateStandardDeviation"> causing the sigma estimate as well as the chip
   type annotation for non-GladModels to be missing.
  
 * readDataFrame() of AffymetrixProbeTabFile did not return the correct number
   of rows if there were missing cells, which there are.
  
 * applyRows() and lines() of CopyNumberRegions did not handle cases with zero
   regions.
 
DEPRECATED AND DEFUNCT:
  
 * CLEAN UP: Removed obsolete getDescription() from AffymetrixFileSet.
  
 * CLEAN UP: Removed obsolete getSibilings() from AffymetrixCelSet.
  
 * CLEAN UP: Removed obsolete gcrmaSummary() and rmaSummary().
  
 * DEFUNCT: All getCellMap() are now defunct; use getUnitGroupCellMap().
  
 
Version: 0.9.1 [2008-04-04]
  
 * Now setCdf() also reports on the two incompatible chip types involved
   if trying to set a CDF that is not compatible with a CEL file.
  
 * Added getMainCdf() for AffymetrixCdfFile for retrieving the
   "main" CDF given a monocell CDF.
  
 * Now the standard deviation across all CNs in a chromosome is calculated
   using a robust first-order difference estimator, which will make the
   estimate much less affected by copy-number changes.

 * BETA: Added estimateSds() to CopyNumberChromosomalModel for estimating
   the standard deviation of the raw CNs (log2-ratios) robustly and so
   that change points have minimal impact. This is done by using a
   first-order difference variance estimator.  The reading of the data
   can definitely be made faster, but at least it works for now.  Added
   redundancy tests for this based on the 10K and the 100K chip types.
  
 * BETA: Added static method allocateFromCdf() for AffymetrixCelFile.
  
 * BETA: Added readDataFrame() for AffymetrixCdfFile (SLOOOOW! but will
   be faster when the underlying function in 'affxparser' is updated).
  
 * BETA: Added getUnitGroupCellChromosomePositionMap() to both
   AffymetrixCdfFile and ChipEffectFile.
  
 * BETA: Added isUnitGroupCellMap().
  
 * BETA: Added matrixBlockPolish().
 
BUG FIXES:

 * BUG FIX: The ArrayExplorer would generate image files to a directory
   under reports/<dataSet>/<tags>,<tags>/..., i.e. the tags where
   replicated.  This is a bug introduced in the latest release.  Thanks
   to
  
 * BUG FIX: getTableOfArrays() of AffymetrixCelSetTuple returned the
   incorrect array indices for the 2nd chip type if different arrays
   in the two sets.
  
 * BUG FIX: Regular expression pattern 'a-Z' is illegal on (at least)
   some locale, e.g. 'C' (where 'A-z' works). The only way to specify
   the ASCII alphabet is to list all characters explicitly, which we now
   do in all methods of the package.  See the r-devel thread
   "invalid regular expression '[a-Z]'" on 2008-03-05 for details.
  
 * BUG FIX: extractMatrix(..., cells=NULL), the default, would throw
   'Error in order(cells) : argument 1 is not a vector'.
  
 * BUG FIX: getUnitIntensities() would not pass arguments '...', e.g.
   'stratifyBy', to readUnits() for AffymetrixCdfFile.  Thanks to
   Tim Keighley, CSIRO, Sydney, for reporting this.
  
 * BUG FIX: Calling readUnits() of an AffymetrixCdfFile without specifying
   the 'units' argument gave an error.  Thanks again Tim Keighley.
  
 * BUG FIX: Calling readUnits(..., units=cdfUnits, stratifyBy=stratifyBy)
   twice with different 'stratifyBy' arguments and with a 'cdfUnits' list
   structure containing the identical set of unit names, would cause
   readUnits() to incorrectly return cached results from the previous call.

DEPRECATED AND DEFUNCT:
  
 * CLEAN UP: Removed the backward compatibility patch from 2007-01-10 that
   made fromDataFile() of ChipEffectFile to add missing tags. If anyone
   still has such old chip effect files lying around, they have to either
   add the tags manually or reanalyze the data if they want the fullnames
   of the chip effect files to match the fullnames raw data files.
  
 
Version: 0.9.0 [2008-02-29]
  
 * UPDATE/ROBUSTNESS: Now AromaUnitTabularBinaryFile:s stores the
   chip type in the file footer.  This allows us to identify the
   correct file gives a full chip type.  Because of this update,
   old UFL and UGP files become incompatible with the class and new
   version have to be downloaded.  The chip type can be queried by
   getChipType().  It is now also asserted that the number of units
   in the file match the number of units in the corresponding CDF.
  
 * TIME OPTIMIZATION: Now RmaPlm and ExonRmaPlm turn to median polish
   if there are more than 500 cells *and* 6 arrays in the unit group.
   Option: aroma.affymetrix.settings$models$RmaPlm$medianPolishThreshold.
   Moreover, if the unit group is ridiculously large (5000 cells), the
   unit group is skipped and all returned estimates are NAs.
   Option: aroma.affymetrix.settings$models$RmaPlm$skipThreshold.
  
 * TIME OPTIMIZATION: Now as.character() for AffymetrixCelSet reports
   time stamps only for data set with less than 500 arrays.
   Option: aroma.affymetrix.settingsoutput$timestampsThreshold.
  
 * UPDATE: Annotation data directories starting with a period are no
   longer searched when looking for annotation data files.
  
 * UPDATE: GcContentNormalization would only normalize SNP units but
   now also CN probes are normalized.
  
 * UPDATE: Now a CnPlm with combineAlleles=TRUE also handles SNPs
   with six groups; they occur at least once in a custom SNP CDF.
  
 * GENERALIZED: Now SNPs and CN probes are infered from the CDF unit
   type and no longer from the unit names.
  
 * Added boxplotStats() to ChipEffectSet for calculating NUSE or RLE
   boxplot statistics (also on a subset of arrays).
  
 * Added getUnitTypes() for AffymetrixCdfFile.
  
 * Added extractMatrix() and extractDataFrame() to Parameter{File|Set},
   i.e. subclasses ChipEffect{File|Set} and Firma{File|Set} got it too.
  
 * Added published paper to citation("aroma.affymetrix").
  
 * CLEANUP: Now byName() can be used everywhere fromName() can be used.
   Same for byChipType() and fromChipType().

 * MEMORY OPTIMIZATION: Now importFromDChip() for CnChipEffectSet uses
   much less memory when infering the cell indices.
 * Updated importFromDChip() for CnChipEffectSet so that it imports data
   exported by more recent versions of dChip.  In recent versions the
   standard-error columns are named '*SE' whereas before it were '*SD'.
   In either case, standard errors were exported (confirmed by author).
   
MAINLY FOR DEVELOPERS:
  
 * CLEANUP: Renamed getMonoCell() to getMonocellCdf() and
   createMonoCell() to createMonocellCdf(), because the former had
   strange names.
  
 * CLEANUP: Renamed usage of getCellMap() to getUnitGroupCellMap().
   For backward compatibility, the old ones remain for a while.

 * BETA: Added static importFromApt() for CnChipEffectSet.
  
 * BETA: Added classes AffymetrixAptSummaryFile and AffymetrixCnChpFile.
  
 * BETA: Added class AromaUfcFile.
  
 * BETA: Added classes DChipChpFile and DChipChpSet.
  
 * BETA: Added class AlleleSummation.

BUG FIXES:

 * BUG FIX: The methods for calculating boxplot statistics did not
   handle "merged" CDF units correctly giving incorrect results.
  
 * BUG FIX/ROBUSTNESS: It was possible to set a non-compatible
   CDF when using static fromFiles() of AffymetrixCelSet.
  
 
 * BUG FIX: getTimestamp() for AffymetrixCelFile would return NA for
   Calvin files.  Now they are also supported.
  
 * BUG FIX: getCellIndices() of CnChipEffectFile would return an error
   if 'units==NULL'.
  
 * BUG FIX: Since 'affy' defines standardGeneric("colnames") and
   S3 methods are not found by such S4 generic functions, we avoid
   that method name, and instead use getColumnNames().
  
 
Version: 0.8.3 [2007-12-18]
  
 * UPDATE: Package patches installed by downloadPackagePatch()
   are now stored in ~/.Rpatches/ (previously in ./patches/).
   Thus, patches will be applied regardless of working directory.
  
 * UPDATE: Changed fit() for FirmaModel to operate as fit() for
   ProbeLevelModel, where the units are read in in chunks and
   operated on over all chips, instead reading and operating
   chip-by-chip.  Default summary is now the median residual
   instead of 1-UQR of weights.  The added tags will reflect what
   settings are used.
  
 * DEVEL: Added summaryOfUnits() for AromaUflFile.

BUG FIXES:

 * BUG FIX: extractMatrix() of ChipEffectSet was broken (due to an
   internal bug in getCellMap() of ChipEffectFile).
  
 * BUG FIX: When calling fit() on a ProbeLevelModel for chip type
   where no monocell CDF exists, an exception like "Could not create
   AffymetrixCdfFile object. No CDF file with that chip type found:
   GenomeWideSNP_6,Full,monocell" would be thrown.  This is due to
   a bug introduced in previous version when trying to make sure
   custom CDFs are carried down more consistently.  Now getMonoCell()
   of AffymetrixCdfFile will create the monocell CDF, if missing.
 
 
Version: 0.8.2 [2007-12-10]
  
 * Added argument 'cdf' to static fromName() of AffymetrixCelSet.
   When using this argument, the 'chipType' argument is optional,
   and the returned CEL set will be using the specified CDF.
  
 * In general, there is now better support for tagged CDFs.  For
   instance, AffymetrixCdfFile$fromName("HuEx-1_0-st-v2", tags="core")
   can be used to locate 'HuEx-1_0-st-v2,core.CDF'.
  
 * UPDATE: Now output sets of a FirmaModel are stored in firmaData/.
   Previously they were stored under modelFirmaModel/.
  
 * UPDATE: Updated AffymetrixNetAffxCsvFile and AromaUflFile to
   better import fragment-length information from NetAffx files.
  
 * ROBUSTNESS: Now getGenomeInformation() of AffymetrixCdfFile asserts
   that the located GenomeInformation annotation file is compatible
   with the CDF.  Same for getSnpInformation().  Currently this can
   only be asserted for UGP & UFL annotation files.
  
 * CONSISTENCY: Now getChipEffectSet() of ProbeLevelModel infers the
   monocell CDF from the CDF of the input data set and uses that when
   retrieving the chip-effect CEL set, not only when creating the set
   from scratch, but now also overriding the CDF according to the CEL
   header of existing sets.  In other words, if the CDF is overridden
   for the input data set, it will also be overridden (with the
   corresponding monocell CDF) in the chip-effect set.
  
 * CLEAN UP: Went through all classes where applicable and updated
   so that getTags() and getAsteriskTags() work properly.  The
   latter was also renamed from getAsteriskTag() to getAsteriskTags()
   to indicate that it can actually return a multiple tags.
  
 * CLEAN UP: Since much of the feature we used in 'affyPLM' moved to
   'preprocessCore', packages 'affyPLM' (and 'affy') are no longer
   required by default.  As with 'gcrma', the 'affy' package is only
   "suggested" and will be requested if need, e.g. when doing using
   one of background correction methods.
  
 * DEVEL: Renamed all getAsteriskTag() methods to getAsteriskTags().
  
SOFTWARE QUALITY:

 * Package pass R CMD CHECK on R v2.6.1 patch (WinXP).

 * All testScripts/system/ scripts pass as well. Total processing
   time right of these scripts is ~18 hours.
 
BUG FIXES:

 * BUG FIX: Tags from the input data set of FirmaModel were lost.
  
 
Version: 0.8.1 [2007-12-01]
  
 * DEPENDENCIES: Package now requires R v2.6.0 or newer.  The main reason
   for this is so we can move away from outdated package dependencies.
  
 * NOTE: For AllelicCrosstalkCalibration and FragmentLengthNormalization,
   the default is now to exclude units/cells on sex chromosomes from
   the model fitting (in order not shrink XX and XY samples towards
   each other).  For instance, AllelicCrosstalkCalibration argument
   'subsetToAvg' defaults to '-XY' which automatically look up all units
   and then cells that are on ChrX and ChrY.  For this to work, there
   must be a genome information file for the chip type. Note, '-XY' will
   work also on chip types for which there is no ChrY, e.g. Mapping250K_Nsp.
   The output data set will be get the extra tag '-XY' whenever this
   type of subsetting is used.  To fit with all units, use 'subsetToAvg=NULL'.
  
 * MODEL UPDATE: The AllelicCrosstalkCalibration method would,
   if 'targetAvg' was specified (default), rescale the probe signals
   such that the average of *each* allele-pair group would equal
   the target average (default =2200).  However, this approach would
   make it hard to correct for other kinds of systematic effects,
   e.g. varying mixing proportions of target DNA from different
   enzymes.  For instance, on the GenomeWideSNP_6 chip type the
   symptom could be that raw CN estimates for CN probes would be
   biased compared with SNP units.  The default, for these SNP & CN
   chip types ("5.0" & "6.0") is now to rescale all signals on the
   array together, i.e. basically a median scale normalization.  For
   the SNP only chip types ("10K", "100K" & "500K") the default is to
   rescale by group.
  
 * UPDATE: Updated AffymetrixNetAffxCsvFile to recognize enzyme
   fragment annotation data for the new GenomeWideSNP_6 CSV files.
 
 * CLEAN UP: Moved the following methods to R.utils: copyFile(),
   dataFrame(), isEof(), and reassignInPackage().
  
 * CLEAN UP: normalizeAverage.{matrix,list}() is now instead in
   the aroma.light package.
  
SOFTWARE QUALITY:

 * Package pass R CMD check on R v2.6.1 patched as well as all
   redundancy tests in testScripts/.

 * TESTS: Added test script for HuEx-1_0-st-v2 by Elizabeth Purdom.
  
BUG FIXES:
  
 * BUG FIX: The multi-enzyme model implemented was not the one in mind;
   The correction for the multi-enzyme data points was not right.
   The example(normalizeFragmentLength) has been updated to also display
   the normalized log-ratios (as a function of fragment length as well
   as they densities).  That revealed the bug.  The example also tests
   the case for non-aliquot mixing proportions between enzymes. This
   is indeed "automagically" corrected for by the model itself, i.e.
   there is no need to estimate the mixing proportions explicitly.
  
 * BUG FIX: The AllelicCrosstalkCalibration introduced in previous
   version was broken for 10K (and possibly also for 100K and 500K).
  
 
Version: 0.8.0 [2007-11-25]
  
 * Updated FragmentLengthNormalization to normalize data for which
   more than one enzyme was used to digest the DNA. See class for
   model constraints and assumptions. Tested on GenomeWideSNP_6 data.
  
 * Now argument 'chromosome' for getUnitsOnChromosome() needs to be
   specified explictly. Before its default was '23'.
  
 * Now the asterisk tags ('*') of the ProbeLevelModels are no longer
   interpreted in the constructor, but by getTags() in the Model class.
  
 * MEMORY OPTIMIZATION: getCellMap() and getCellIndices() for
   ChipEffectFile et al. now extracts data in chunks.
  
 * BETA: Added low-level methods fitWHRCModel() and fitWHLAPLM().
 
 
Version: 0.7.2 [2007-09-30]
  
 * Now the main HTML file for ChromosomeExplorer is ChromosomeExplorer.html,
   which is in analogue to how the ArrayExplorer works.  This HTML now
   loads to a different Javascript file with a different name so that
   already existing index.html ChromosomeExplorer files will still work.
  
 * By default, all CopyNumberSegmentationModel plots do now display
   non-robust and robust estimates of the standard deviation of the
   raw CNs across the complete genome.  Note that this is not done
   segment by segment, so if there are alot of aberrations then these
   estimates will be biased.

 * ROBUSTNESS: Now getAverageFile() of AffymetrixCelSet detects if an
   average file has been deleted between calls and recalculates it,
   if missing.
  
 * BETA: Did some "behind the scenes" restructuring of the
   CopyNumberSegmentationModel by adding an even simpler superclass
   ChromosomalModel, allowing for simpler types of modelling along
   the chromosomes.

SOFTWARE QUALITY:

 * Package pass R CMD check on R v2.6.0 beta and all of the redundancy
   tests.  The redundancy tests are now available under testScripts/
   in the package directory.

BUG FIXES:
    
 * BUG FIX: Forgot to update ExonRmaPlm to handle compatibility issues
   with affyPLM/preprocessCore. See below.
  
 * BUG FIX: The CopyNumberSegmentationModel:s did not support paired
   copy-number analysis by specifying references files explictly.
   To do this, pass an additional list of CnChipEffectSet:s via
   constructor argument 'refTuple'.  This list my contain the same
   chip types, and each chip type must contain exactly the same number
   of files.  Note, the hashcode-generated hexadecimal tag added to
   the save CopyNumberSegmentationModel results, but also as part of
   the ChromosomeExplorer image files, will be different in this new
   version, meaning the package will not detect already existing
   segmentation estimates.  You can always one run chromosome, check
   the new hashcode, and rename existing files to have the same one.
  
 * BUG FIX: Before duplicated tags were removed using unique(), but that
   would also remove duplicated tags that were not "neighbors", e.g.
   the 2nd "-X" tags in "ACC,-X,RMA,A+B,FLN,-X" was removed.  Now
   only duplicated neighboring tags are removed, e.g. "-X,-X,-X".
   
DEPRECATED AND DEFUNCT:
  
 * CLEAN UP: Moved several classes to aroma.affymetrix.extras that
   are haven't been updated in a long time and are likely to be broken.
   This was done in order make this package easier to maintain. If this
   broke something for you, please contact me.
  
 
Version: 0.7.1 [2007-09-18]
  
 * Now fit() of CopyNumberSegmentationModel reports timing
   information for each chromosome fitted when in verbose mode.
  
 * Now importFromAffymetrixNetAffxCsvFile() of AromaUgpFile averages
   positions if multiple positions were available for a particular unit.
  
 * ROBUSTNESS: Made createFrom() of AffymetrixCelFile fail safe,
   that is, the destination file will not be created unless it
   is complete.  This is done by first create/writing to a temporary
   file which is then renamed at the end. This should minimize the
   risk of creating incomplete CEL files.
  
 * ROBUSTNESS: Added internal fileCopy() which copies a file via
   a temporary file which is renamed.  All file copying in the
   package is now done via this method.
  
 * BETA: Added trial version of ScaleNormalization.
  
 * BUG FIX: Due to a migration of code from affyPLM to preprocessCore,
   the fit function returned by getFitFunction() would not work with
   affyPLM >= 1.13.9.  Now getFitFunction() adopts to the version of
   affyPLM/preprocessCore installed.  If preprocessCore v0.99.16 or
   newer is available, that is used, otherwise affyPLM v1.13.8 or older
   is used. This has been veried to work on i) R v2.5.1pat with
   affyPLM v1.12.0, and R v2.6.0alpha with preprocessCode v0.99.16.
   (affyPLM v1.13.6).

BUG FIXES:
    
 * BUG FIX: The workaround storing single-probe sdTheta estimates
   as a small value was set for single-*chip* not probe cases.
  
 * BUG FIX: getFragmentLengths() of UflSnpInformation would thrown
   an error "Unknown fields: fragmentLength".  Now getDataColumns()
   returns the correct names.
 
DEPRECATED AND DEFUNCT:
  
 * CLEAN UP: Removed obsolete copyFile() from AffymetrixFile in
   favor of copyTo() in GenericDataFile.
  
 
Version: 0.7.0 [2007-09-15]
  
 * Now it is possible to specify the genome used for segmentation and
   plotting. This can be done either via argument 'genome' in the
   constructor or by setGenome() of CopyNumberSegmentationModel.
   A corresponding <genome>(,<tags>)*,chromosomes.txt file should be
   put in annotationData/genomes/<genome>/. If not found there, the
   file is searched for in the annotationData/ directory installed
   with the package. If the file is not found, setGenome() will give
   an error.  If not specified, the genome defaults to "Human".
   The above file specifies the number of bases per chromosome,
   which is used when plotting chromosomal data.  The previous file
   'hgChromosomes.txt' is now deprecated and obsolete.
  
 * Now CopyNumberSegmentationModel only adds cytobands to genomes
   for which cytoband information is available.  Currently this is
   hardwired only the "Human" genome. For all other genomes, there
   will be no cytoband.
  
 * Now AllelicCrosstalkCalibration corrects also non-SNP PM cells by
   substracting a global offset and rescaling towards target average.
   The global offset is calculated as the weighted average of all
   allelic offsets. SNP probes are calibrated in the same way as before.
  
 * Updated all places with SNP regular expression "^SNP" to "SNP_" in
   order to also match units named "AFFX-SNP_...".
  
 * SPEED UP: Now getCellMap() of ChipEffectFile caches (large) results
   to file.
  
 * SPEED UP: Now getOutputDataSet() of FragmentLengthNormalization set
   and pass down 'mergeStrands' and 'combineAlleles' to ditto of the
   super class, if applicable.  This way we avoid having to infer those
   arguments from the contents of the files.  This gives an significant
   speed up for large chip types.
  
 * ROBUSTNESS: Now the RmaPlm fit function detects cases where a probe
   get zero weight for all arrays. In such (rare) cases, parameter
   estimates equals NAs. Before an LAPACK error was thrown.
  
 * ROBUSTNESS: Added validate that the 'name' of an AffymetrixCelSet
   and AffymetrixCelFile is of at least length one.
  
 * ROBUSTNESS: Now isDone() of Transform throws an error if too many
   output files are found. Before it used to return FALSE.
  
 * WORKAROUND: If there is only one probe, then fit function of AvgPlm
   would return theta=y:s, and sdTheta=0:s.  However, when searching
   for units to do, we test (sdTheta <= 0).  The workaround is to store
   the smallest float available instead of zero.
  
 * BETA: Added GenericDataFile, GenericDataFileSet, and GenericTabularFile.
  
 * BETA: Added AffymetrixTabularFile, AffymetrixNetAffxCsvFile,
   AromaUgpFile, and AromaUflFile.
  
 * BETA: Added UflSnpInformation and UgpGenomeInformation
   interfacing to UGP and UFL files.
  
 * BETA: Added AvgPlm, AvgSnpPlm, AvgCnPlm.

SOFTWARE QUALITY:

 * Package passes R CMD check on R v2.5.1pat & R v2.6.0alpha on Windows XP.
   It also passes all redundancy tests on Linux.

BUG FIXES:

 * BUG FIX: Now more effort is made to ensure that all CEL files are
   generated with an upper-case filename extension (*.CEL) and not (*.cel).
   Thanks Jeremy Silver for reporting problems on this.
 
 
Version: 0.6.2 [2007-09-07]
  
 * Now setCdf() of AffymetrixCelSet throws an (informative) error message
   whenever one tries to use an ASCII CDF file. This behavior can be
   changed by setting rule 'aroma.affymetrix.settings$rules$allowAsciiCdfs'
   to TRUE in the options. The reason is that working with ASCII CDF files
   is extremely slow and memory inefficient. Use affxparser::convertCdf()
   to convert a CDF into a binary format.
  
 * Updated AllelicCrosstalkCalibration internally.  It now also stores
   the model parameter estimates to file (using a plain save() file format).
  
 * MEMORY OPTIMIZATION: Instead of doing unlist(getCellIndices(cdf, ...),
   use.names=FALSE), we can now do getCellIndices(cdf, useNames=FALSE,
   unlist=TRUE), which is much more memory efficient, e.g. for the
   GenomeWideSNP_6 chip the former uses 25x more memory, which means
   that instead of using 1.4GB we can get away with 60MB.
  
 * CLEAN UP: All calibrateAllelicCrosstalk() methods are now removed.
   Use the AllelicCrosstalkCalibration class instead.
  
SOFTWARE QUALITY:

 * Package passes R CMD check on R v2.5.1 and R v2.6.0 devel on Windows.
   All redundancy tests works on Linux.
 
 
Version: 0.6.1 [2007-09-05]
  
 * Added support for fitting copy-number regions using the (fast)
   Circular Binary Segmentation (CBS) method of Venkatraman et al. (2007).
   The method is implemented by the new CbsModel class.  Consider this
   class to be very much in a beta version.
  
 * Added super class CopyNumberSegmentationModel, which provides most of
   the framework to fit and plot segmentation models. By subclassing
   this class, new segmentation methods can be added. Current subclasses
   are GladModel and CbsModel.  ChromosomeExplorer was updated to handle
   multiple segmentation methods.
  
 * Now the startup message when loading the package is generated with
   packageStartupMessage() so that it can be suppressed.
  
 * Put more effort in generating more consistent hash codes that becomes
   part of the filenames of the averaged files.  This modification is
   likely to lead to new hashcodes, and there for new filenames such
   that aroma.affymetrix will not detect existing "average" files.
   In turn, this will mean that stored results from GladModel will
   not be recognized (unless you rename files with the new hashcodes).
  
 * Added a "patch" to make sure that there is rowMedians() supporting
   missing values by looking for the correct version of Biobase,
   R.native or just an apply() notes.  This does unfortunately mean
   that generated hashcodes my be different so certain average CEL
   files will be recalculated, and in turn segmentation results will
   be regenerated.
  
 * PACKAGE DEPENDENCIES: Made R.native an "Supports" package, since it
   is only used for rowMedians() in case the right Biobase version is
   not availble.  R.native is now optional.

BUG FIXES:

 * BUG FIX: getAverageFile() of AffymetrixCelSet had 'na.rm=FALSE'
   by default, which caused a lot of missing values in the average.
   In turn, this cause for instance raw CNs to become missing values.
  
 * BUG FIX: When calling process() on a GcRmaBackgroundCorrection,
   an exception would be thrown with "bgAdjustGcrma() is deprecated.
   Please use the GcRmaBackgroundCorrection class".  The same happend
   with OpticalBackgroundCorrection.  This was due to a typo introduced
   in v0.5.3 when making the underlying functions deprecated.  Thanks
   Jeremy Silver for troubleshooting and reporting this.
 
DEPRECATED AND DEFUNCT:
  
 * CLEAN UP: Deleted obsolete /inst/chromosomeExplorer/ from source.
  
 * CLEAN UP: Removed some obsolete affxparser patches.
  
 
Version: 0.6.0 [2007-08-17]
  
 * Steps have been taken to support working with Calvin CEL files.  This
   is still in testing, but from first tests it looks like it is working.
  
 * Now calculateResidualSet() of ProbeLevelModel only loads probe-affinity
   estimates if needed, i.e. if residuals are already calculated this
   function will return faster now.
  
 * Now createFrom(..., methods="create", clear=FALSE) of AffymetrixCelFile
   will first create an empty file, and then copy all CEL data to the
   new file.  This way createFrom(..., methods="create", clear=FALSE)
   and createFrom(..., methods="copy", clear=FALSE) should give CEL
   files containing the same data.  createFrom() also accepts a vector
   of options in 'methods' (renamed from 'method') which will be tried
   in order until success.
  
 * Now getImage() of AffymetrixCelFile defaults to no interleaving,
   i.e. argument defaults to interleaved="none".  The reason for this
   is that the previous default "auto" did not work too well and
   sometimes turned on interleaving although not needed.  So, now
   one has to use interleaved="auto" ("v" or "h") when for instance
   getting images for spatial PLM residuals where an PM-only fit was
   done to a chip with MMs (otherwise every 2nd line will be blank).
   This also affects the ArrayExplorer; you pass the 'interleaved'
   argument via the process() call.
  
 * Added support for dChip's 'snp6.0 genome info hg18.txt' file.  Note,
   this only contains informations for SNPs, not CN probes.
  
 * MEMORY OPTIMIZATION: calculateResidualSet() of ProbeLevelModel does
   part of the work in chunks.
  
 * MEMORY OPTIMIZATION: Made getCellIndices() of AffymetrixCdfFile more
   memory effiencent by reading and transforming data in chunks.
  
 * MEMORY OPTIMIZATION: Made findUnitsTodo() of ChipEffectFile scan
   for units in chunks.  This would bring done memory usage to about
   5% of what is used to consume.
  
 * MEMORY OPTIMIZATION: Now getAlleleProbePairs() of AffymetrixCdfFile
   processes the CDF in chunks in order to save memory.  Before,
   processing the GenomeWideSNP_6.CDF would consume 1.5-2.0GB RAM, but
   now it is using less than 500MB.
  
 * MEMORY OPTIMIZATION: ArrayExplorer now garbage collects after each
   image written.  That save a few hundred MB.
   
 * CLEAN UP: Removed findUnitsTodo() from ExonChipEffectFile, because it
   gave the same result as the one in super class ChipEffectFile.
  
SOFTWARE QUALITY:

 * Package passes R CMD check on R v2.5.1 and R v2.6.0 devel.
  
 * Package passes all redundancy tests.

BUG FIXES:
  
 * BUG FIX: Removed internal trial encoding function added by mistake
   to the previous version.  
 
 
Version: 0.5.6 [2007-08-10]
  
 * Package passes R CMD check on R v2.5.1 and R v2.6.0 devel.
  
 * AffymetrixFileSet class defines lapply(), which causes lapply()
   to redefined as a generic function, which in turn gives some
   overhead to "standard" lapply() calls due to method dispatching.
   All standard lapply() calls are now called as base::lapply().
   Benchmarking: This changes makes fit() on SNP 10K roughly 10% faster.
  
 * Now all generated CEL files are written with upper-case filename
   extension (*.CEL).  The main reason for this is that some other
   software don't recognize CEL files with lower-case extension (*.cel).
   Existing CEL files that are in lower case (*.cel) and that are
   generated by the package are renamed to upper case (*.CEL).
   Same thing for generated CDF files.

BUG FIXES:
  
 * BUG FIX: ArrayExplorer assumed identical sample names and color maps
   across chip types and plots.  Now the set of samples and color maps
   displayed are unique for each chip type.
 
 
Version: 0.5.5 [2007-08-03]
  
 * MISC: Keeping the normalizeAverage() that was moved to aroma.light,
   so that the the package works with aroma.light v1.4.x that comes
   with the BioC release.  This means that it is only 'aroma.affymetrix',
   'aroma.apd', and (optional) 'R.native' that are not on CRAN/BioC.
  
 * This version was used at the BioC2007 practical.
 
 
Version: 0.5.4 [2007-08-02]
  
 * Renamed static fromName() of AffymetrixCelSet to byName().
  
 * Renamed fromChipType() of AffymetrixCdfFile to byChipType().
  
 * Some of the dependencies were to weak in the DESCRIPTION file.
   Added explicit version dependencies also for Suggests and Imports
   packages.

BUG FIXES:
    
 * BUG FIX: getCellMap() of ChipEffectFile would give an error if
   verbose output was on.
 
 
Version: 0.5.3 [2007-07-13]
  
 * Now more verbose output is generated when a monocell CDF is created
   in the background.
  
 * Added getFileFormat() to AffymetrixCdfFile and AffymetrixCelFile.
   These are also reported by the corresponding print() method.
  
 * Made bgAdjustOptical(), bgAdjustRma(), and bgAdjustGcRma() deprecated.
   If used, an error will be thrown.  Use the Optical-, Rma-, and
   GcRmaBackgroundCorrection classes instead.
  
 * MEMORY OPTIMIZATION:  Includes a patch to affxparser:::.initializeCdf()
   to make it much more memory efficient, e.g. when writing the CDF
   header unit names, it could consume >1.5GB RAM, whereas now it is
   in the order of 100-200MB.  This patch will go away as soon as
   the affxparser package incorporates it.
  
 * MEMORY OPTIMIZATION:  Includes a patch to base::matrix() that does not
   create an extra copy when assigned a new value to a cell, e.g. the 2nd
   statement in the following would force a new copy of the matrix:
   x <- matrix(0, 5000,5000); x[1,1] <- 1;  Thanks to Luke Tierney for
   troubleshooting and suggesting a patch; there are no immediate plans
   to include this patch in 'base' though.

SOFTWARE QUALITY:

 * Package passes R CMD check on Rv2.5.1 (and R v2.6.0 devel).
  
 * Package passes all (#1 and #2) redundancy test sets available on
   the group page.  This was confirmed on R v2.5.1 on WinXP (1.5GB RAM).
  
BUG FIXES:
  
 * BUG FIX: Now (private) createMonoCell() of AffymetrixCdfFile will
   build the monocell CDF to a temporary filename, and only when it is
   done, rename it to the final *,monocell.cdf filename.  This will
   lower the risk for creating an invalid CDF, which for instance can
   happen if we run out of memory.  Reading invalid CDFs will core
   dump R due to the affxparser and the Fusion SDK package.
  
 * BUG FIX: The memory usage of fit() of the FirmaModel would increase
   linearly with the number of arrays processed.  This was because
   read results where cached for each of the FirmaFile:s.  Thanks Mark
   Robinson for reporting on this.
  
 * BUG FIX: getOutputDataSet() of Transform would give "Error in
   fromFiles.AffymetrixCelSet(static, path = path, pattern = pattern,:
   formal argument "checkChipType" matched by multiple actual arguments".
   This was due to the recent adding of 'checkChipType=FALSE'.  Fixed
   by adding 'checkChipType=FALSE' to fromFiles() of ChipEffectSet.
   Thanks Jeremy Silver at WEHI for report and troubleshooting this.
 
 
Version: 0.5.2 [2007-06-25]

BUG FIXES:

 * BUG FIX: When getOutputDataSet() retrieved the output data set, the chip
   type of the CEL files would be validated against the path name, also when
   then CDF of the input set was overriden.  Now the output data set is
   setup using 'checkChipType=FALSE'.  Thanks Mark Robinson for
   troubleshooting this.
 
 
Version: 0.5.1 [2007-06-12]
  
 * Moved normalizeAverage() to aroma.light.
  
 * Replaced all require(<pkgname>) with require("<pkgname>").

SOFTWARE QUALITY:

 * Package passes R CMD check on Rv2.6.0 devel.  This new version of
   R CMD check does a lot more validation on the code and several
   potential problems were found this way.
 
BUG FIXES:
  
 * BUG FIX: When argument 'transforms' to getImage() of AffymetrixCelFile
   wasn't a list, then "Error: argument "transform" is missing, with no
   default" was thrown.  Thanks Karen Vranizan, UC Berkeley for reporting
   this problem.
  
 * BUG FIX: If an Affymetrix probe tab file is not found for the chip type,
   computeAffinitities() of AffymetrixCdfFile would throw "Error in
   paste(..., sep = sep, collapse = collapse): object "pattern" not found"
   instead of an intended and more information error.
  
 * BUG FIX: getSiblings() for AffymetrixCelSet was broken.
  
 * BUG FIX: Called getFile(ces, ...) instead of  getFile(this, ...) in
   fitGlad() of CnChipEffectSet.  If the GladModel was used to fit the
   GLAD model this bug has not affected the modelling.
  
 * BUG FIX: Used getFileName() instead of getFilename() in exportToAPT()
   of SnpChipEffectSet.
  
 
Version: 0.5.0 [2007-05-10]

 * getProbeAffinityFile() of ExonRmaPlm did not return the correct subclass.
  
 * Added default zoom levels to updateSamplesFile() for ChromosomeExplorer.
   This is applies the first time process() is called.
  
 * Removed dependency of the R.image package by removing writeSpatial()
   for the AffymetrixCelFile class.  Use writeImage() instead.
  
 * Now patchPackage(..., deleteOld=TRUE) removes not only old patches, but
   also patches that are older than the package itself.  Thus, when loading
   the package, all old patches are automatically removed.
  
 * Added argument 'apply=TRUE' to downloadPackagePatch() so that downloaded
   patches are applied immediately after being downloaded.

SOFTWARE QUALITY:

 * Package passes R CMD check on Rv2.5.0 (and R v2.4.1).
  
 * Package pass redundancy tests on R v2.5.0 (and R v2.4.1). This was
   confirmed to work on Windows XP.
  
BUG FIXES:
  
 * BUG FIX: calibrateAllelicCrosstalk() for AffymetrixCelFile would output
   filenames containing only the name but not the tags.
  
 * BUG FIX: If no valid timestamp was identified in the CEL header by
   getTimestamp() of AffymetrixCelFile, then as.character() would give
   "Error in sprintf(fmt, ...) : zero-length argument".  Now it returns
   NA instead as a fall back if no valid timestamp is found.  Thanks
   Mark Robinson, WEHI, for reporting this.
  
 * BUG FIX: getRegions() and getLog2Ratios() of GladModel would give an
   error if only a subset of the chromosomes where queried.
 
 
Version: 0.4.9 [2007-04-22]
  
 * BUG FIX: Added missing getExclCells() to QuantileNormalization.
   Thanks Elizabeth Purdom for the report.
 
 
Version: 0.4.8 [2007-04-19]
  
 * Now non-positive signals are given weight zero when being fitted
   in the IWLS algorithm for the log-additive model of RmaPlm.
   This requires affyPLM v1.11.14.  Thanks Ben Bolstad for adding
   support for weights.
  
 * BUG FIX: getChipEffectSet() and getProbeAffinityFile() of the
   ExonRmaPlm class did not set the 'mergeStrands' parameter.
   Thanks Elizabeth Purdom for the fix.
 
 
Version: 0.4.7 [2007-04-12]
  
BUG FIXES:
  
 * BUG FIX: fromFiles() of AffymetrixCelSet would give error "Exception:
   Pathname not found: annotationData/samples" if that directory was
   missing.  Now it is instead created.
  
 * BUG FIX: readData() of SampleAnnotationFile would open a text
   connection without closing it.  This would eventually given an
   error about too many open connections.
  
 * BUG FIX: There was a if (TRUE) {} statement in calculateResidualSet()
   that was supposed to be if (!fource) {} in the release version.
  
 * BUG FIX: fromDataFile() of ResidualFile returned an AffymetrixCelFile
   but not a ResidualFile.  This caused getResidualSet() of ProbeLevelModel
   to return a ResidualSet containing AffymetrixCelFile:s.  The same
   bug was found for the WeightFile class.
 
 
Version: 0.4.6 [2007-04-04]  
  
 * Now fromFiles() in AffymetrixCelSet verifies that the CDF being
   assigned to the data set is compatible with the CEL files, i.e.
   have the same number of cells.  The default is to infer the
   chip type from the name of the parent directory of the CEL files,
   but if that chip type is not compatible the chip type according
   to the the first CEL file will be used for the set.
   
BUG FIXES:
  
 * BUG FIX: Loading aroma.affymetrix v0.4.5 (and v0.4.4?) on Windows
   would give: "Error in digest::digest(..., skip = skip, ascii =
   ascii) : unused argument(s) (skip = "auto", ascii = FALSE)".
  
 * BUG FIX: Static fromFiles() in ChipEffectSet did not call ditto in
   super class AffymetrixCelSet but instead the one in grand-parent
   super class AffymetrixFileSet.
 
 
Version: 0.4.5 [2007-04-03]
  
 * Now AllelicCrosstalkCalibration rescales by default allele A and
   allele B signals such  that the get the same averages.
  
 * Added ETA to verbose output of fit() for the ProbeLevelModel.
   
 WORK IN PROGRESS (no guarantees):
  
 * Now RmaPlm:s can handle non-positive signals either by setting the
   to a small number or to ignore them when fitting the PLM.  See code
   of fit function(s) for more details.
  
 * Added AffymetrixTsvFile to read the CNAT v4 "covariate" files.
  
 * Added GcContentNormalization.

BUG FIXES:
    
 * BUG FIX: Probe-affinities were not save, resulting in all zeroes.
   This was due to renaming getProbeAffinites() to getProbeAffinityFile().
  
 * BUG FIX: ChipEffectGroupMerge would catch warnings (like errors)
   when create output CEL files, e.g. when getRelativePath() gave
   an unimportant warning.
  
 * BUG FIX: getFitUnitFunction() for CnPlm was broken for PM-MM
   probe models for single group units, e.g. AFFX units, resulting
   in an error "Argument 'y' must have two dimensions: 3".
  
 * BUG FIX: getFitUnitFunction() of CnPlm did not handle probe
   model "min1(pm-mm)".
 
 
Version: 0.4.4 [2007-03-26]
  
 * Added BackgroundCorrection classes RmaBackgroundCorrection,
   GcRmaBackgroundCorrection, and OpticalBackgroundCorrection.
   These replaces methods bgAdjustRma(), bgAdjustRcRma(), and
   bgAdjustOptical() which are now deprecated.
  
 * The ArrayExplorer class now handles multiple chip types.
  
 * Now inferParameters() of the ChipEffectSet classes is looking
   at the 'intensity' (==theta) field instead of 'stdvs'.  The
   reason for this is that 'stdvs' might be all zeros, e.g. after
   a fragment-length normalization.  
 
WORK IN PROGRESS (no guarantees):
  
 * Added AffymetrixCelSetTuple.
  
 * Added the SpatialReporter class.
  
 * Added the abstract Explorer class.
  
 * Added calculateBaseline() to ChipEffectSet.
  
 * Replaced all occurances of affxparser::copyCel() with createFrom()
   in AffymetrixCelFile.
  
 * Lines of code (excluding comments): grep -v "#" *.R | wc -l => 24902
 
BUG FIXES:
    
 * BUG FIX: clearCache() of AffymetrixCelSet did not clear the
   .readUnitsCache field.


Version: 0.4.3 [2007-03-15]
  
 * Updated the GladModel to only work with chromosome indices (integers).
  
 * Now the GladModel infers the set of possible chromosomes from the
   GenomeInformation file.  This means it handles other genomes than
   the human genome better.
  
 * Updated GenomeInformation to return chromosomes as indices and never
   with 'X' and 'Y' regardless of source.  This is part of a moving the
   package to handle chromosomes as indices so that it will work with
   any genome not just the human.
  
 * Fixed fit() for FirmaModel so that it checks array-by-array
   whether units have been fitted.
  
 * Names of cache files are now made more consistent between
   R versions (and platforms) resulting in more cache hits
   and therefore faster processing.
  
 * Now the package tries to keep the search path of packages in
   such an order that any package known to cause problems to
   aroma.affymetrix if loaded after aroma.affymetrix, will be
   inserted behind aroma.affymetrix in the search path. For example,
   loading the EBImage package after aroma.affymetrix used to cause
   complaints when calling display() on an ArrayExplorer.
   
 * MEMORY OPTIMIZATION: Further optimized memory usage in:
   calculateResiduals() of ProbeLevelModel.
  
 * Lines of code: grep -v "#" *.R | wc -l => 24106
 
WORK IN PROGRESS (no guarantees):
  
 * Added getUnitGroupCellMap() to AffymetrixCdfFile.
  
 * Added code for in-memory attributes to AffymetrixFile object.
   Certain filename tags are interpreted as attributes which are
   set when the AffymetrixFile object is instantiated.
   Note: Attributes are *not* carried over in transforms etc.
  
 * Added the AromaGenomePositionFile class and subclasses
   AromaUgpFile and AromaCgpFile.
  
 * Added extractMatrix() for ChipEffectSet.

BUG FIXES:   

 * BUG FIX: getAverageFile() of AffymetrixCelSet would average the wrong
   set of cells if argument 'indices' was different from NULL.
  
 * BUG FIX: Argument '...' to plotDensity() of AffymetrixCelFile and
   AffymetrixCelSet are no longer passed to identifyCells().
  
 * BUG FIX: calculateResiduals() of ProbeLevelModel would give
   non-zero residuals for cells not fitted by the PLM.
  
 * BUG FIX: plotNuse() and plotRle() did not handle outliers
   correctly.

 * BUG FIX: Changed default filenames for FIRMA scores to
   "%s,FIRMAscores.CEL" rather than "%s,FIRMAresults.CEL" for
   consistency with FirmaModel.
  
 * BUG FIX: extractSnpQSet() would give "Error: object "cleancdfname"
   not found" if the 'affy' package was not loaded.
  
 * BUG FIX: getCellIndices() in CnChipEffectFile would give
   "Error in fcn(.subset2(unit, "groups"), ...) : object "odds"
   not found" for units with other than 1, 2, or 4 groups.
  
DEPRECATED AND DEFUNCT:
  
 * Replaced argument 'moreCells' with 'ram' and removed argument
   'cellsPerChunk' in getAverageFile() of AffymetrixCelSet.
  
 
Version: 0.4.2 [2007-02-28]
  
 * Now patches in patches/aroma.affymetrix/<date>/ are sourced
   when the package is loaded.  To download the latest patches,
   see the package's group page.
  
 * Added argument 'region' to getUnitsOnChromosome() of the
   GenomeInformation class.

BUG FIXES:

 * BUG FIX: setColorMaps() gave "Error in addColorMap.ArrayExplorer(
   this, colorMap, ...) : object "nbrOfColors" not found".
  
 * BUG FIX: The output data set as returned by getOutputDataSet() or
   process() of QuantileNormalization lost the any CDF overridden in
   the input data set.  The only time it did pass down the CDF was
   when process() was called the first time (so that it actually
   normalized the arrays).  The fix was to make getOutputDataSet() in
   Transform to pass down the CDF too.
  
 * BUG FIX: process() of ChromosomeExplorer would give an error saying
   'Error in file(file, ifelse(append, "a", "w")) ... cannot open file
    /*****************...'.
 
 
Version: 0.4.1 [2007-02-22]
  
 * Fixed the warning about "'tzone' attributes are inconsistent". See
   code of as.character() for explanation.
  
 * Now fromFiles() of AffymetrixCelSet accepts argument 'chipType' to
   override any chip type specified in the CEL headers. This is useful
   in case different CEL files refers to different chip types, which can
   be the case for mixed generations of CEL files.  Also added a scan of
   chip types.
  
 * Added support for using Windows shortcuts for CDF files, that is, you
   can use a Windows Shortcut annotationData/chipTypes/Foo/Foo.cdf.lnk
   to link to annotationData/chipTypes/Bar/Bar.cdf, and whenever using
   AffymetrixCdfFile to locate the CDF for chip type 'Foo' you will get
   the CDF for chip type 'Bar', e.g. AffymetrixCdfFile$fromChipType('Foo').

 * The annotation labels at the right of all graphics in the
   ChromosomeExplorer are now made slightly larger.
  
 * Now the table of CNRs generated by the GladModel give links
   to 'hg17' instead of 'hg18' because 'hg17' is the version of
   the dChip genome information files, which are the only one
   currently supported.
  
 * Package passes R CMD check on R v2.4.1 (many empty help pages though).
  
 * Lines of code: grep -v ^# *.R | wc -l => 21772

BUG FIXES:

 * BUG FIX: calculateWeights() of ExonRmaPlm now makes sure residuals
   are calculated first.
  
 * BUG FIX: When creating a monocell, the output did not strip of the tags
   from the chip type, e.g. annotationData/Foo,core/For,core,monocell.cdf
   instead of annotationData/Foo/For,core,monocell.cdf.
  
 * BUG FIX: An update to the GladModel class added to previous version
   would not recognize CEL files with same sample name but different
   tags to belong to the same sample.
  
 * BUG FIX: calculateResiduals() would erase previously calculated
   residual files and not re-create them correctly.
  

Version: 0.4.0 [2007-02-16]
  
 * Package passes R CMD check on R v2.4.1 (many empty help pages though).
  
 * Verified that the current version works on total copy number analysis
   for combined Nsp & Sty chips.  See the aroma.affymetrix group page
   for the example.
  
 * Added trial version of ExonRmaPlm().
  
 * Added trial versions of ResidualSet() and WeightSet().
  
 * Added test for correct directory structure to fromFiles().  This will
   enforce users to use the correct structure so that for instance the
   name of the data set is correctly inferred.
  
 * Added calculateResiduals() to ProbeLevelModel and the ResidualSet
   and ResidualFile classes.
  
 * Now monocell CDF are names <chipType>,monocell.cdf.  Before a dash
   was used instead of a comma. This new style is more in line with
   the <name>,<tags> naming convention used elsewhere in the package.
   Note: Since there are parameter CEL files referring to the old
   <chipType>-monocell, AffymetrixCdfFile$findByChipType() will detect
   this and look for <chipType>,monocell instead. Thus, it should be
   safe to rename the monocell CDF file.
  
 * Now any annotation file for chip type <chipType> may be located
   under annotationData/chipTypes/<chipType>/. This directory
   structure is preferred, because this will allow you to collect
   all your annotation files specific to one particular chip type
   in one place.  You may even put the in subdirectories, e.g.
   Affymetrix/, dChip/ etc.
  
 * From now on all reporters and explorer utilizes the root path
   reports/, and the path to an image file should be
   reports/<dataSetName>/<tags>/<chipType>/<set>/.
   The latter subdirectory was added to avoid potential naming
   conflicts for different reporter or explorer classes.
  
 * Remove package dir doc/.  Not used.
  
 * Added writeChecksum() and validateChecksum() to AffymetrixFile
   to write a checksum file, which later can be validated to the
   content of the file.  This is useful to make sure that
   transferred files have not been corrected (which happend to
   HB while transferring via external HDD).


Version: 0.3.6 [2007-02-05]
  
 * Added support to import dChip-exported CEL files.  See
   importFromDChip() in AffymetrixCelSet.
  
 * Now QuantileNormalization() takes an AffymetrixCelFile as a
   target distribution too, cf argument 'targetDistribution'.
  
 * Now the file cache is organized into subdirectories starting
   with "aroma.affymetrix/".  This makes it easier clear the
   cache.
  
 * Trial: Added SampleAnnotationFile class. File format is not
   settled yet.
  
 * Trial: Removed the 4% left and right extension of xlim from the
   plots and enforced 50px margins outside on both sides.  This
   will make it easier to map the horizontal location in pixels
   to megabases.


Version: 0.3.5 [2007-01-22]
  
 * BUG FIX: Somehow hgChromosomes.txt disappeared from the last
   versions of the package. Readded.
  
 * Now fromChipType() of DChipGenomeInformation recognized
   the Mapping10K_Xba142 genotype information files too, meaning
   getGenotypeInformation() of AffymetrixCdfFile will also
   recognize it.  Same updates were done for dChip SNP
   information files.
  
 * Now the default sample of the ChromosomeExplorer is the first
   sample (and not the 8th, which was left in there while I was
   debugging).  The default chromosome is 1 (not 21st).


Version: 0.3.4 [2007-01-20]
  
 * Passes R CMD check on v2.4.1.
  
BUG FIXES:

 * BUG FIX: When trying to load CDFs (and in some other cases
   too), the GLAD package (and some other packages) wer loaded
   although they are only "suggested" packages.  This was due
   to how the constructor of some classes were implemented.


Version: 0.3.3 [2007-01-17]
  
 * Passes R CMD check on v2.4.0.
  
 * Added classes QualityAssessmentModel, QualityAssessmentSet,
   and QualityAssessmentFile.
  
 * Now createMonoCell() create the CDF in chunks, that is,
   in constant memory.
  
 * Now plot() of GladModel gets the default 'hgChromosomes.txt'
   of the package if it can't be found in annotations/.

BUG FIXES:

 * BUG FIX: For some reason does clearCache() of Object not
   clear out all cached fields. Until I've figured out what
   is wrong, I've added explicit clearCache() to classes using
   cached fields.
  
 * The FragmentLengthNormalization class forgot to clear cache
   after cloning input data set.  This caused the output data
   set to get the same average file as the input data set.
    
 * BUG FIX: createMonoCell() of AffymetrixCdfFile would give
   an errounous mono-cell CDF file due to a recent change.


Version: 0.3.2 [2007-01-07]
  
 * Package pass R CMD check v2.4.0.
  
 * Tested the package from scratch analysis 19 Mapping250K_Nsp
   and 16 Mapping250K_Sty (15 in common) for total copy-number
   analysis. Steps involved: quantile normalization, RMA
   probe-level modelling, PCR fragment-length normalization,
   and combined GLAD modelling.  This was done in WinXP Pro
   on an IBM X61 with 1.5GB RAM.  Memory usage peaked at
   approximately 1GB.
  
 * Some optimization of what is cached in memory and what
   is cached on file.  Only for some data classes for now.
  
 * Replaced old GladModel with new MultiGladModel, which
   is now named GladModel.
  
 * Added AffineCnPlm for completeness.
  
 * The ChromosomeExplorer class now generates a complete
   working ChromosomeExplorer web page.
  
 * WORKAROUND: If 'affy' is loaded after aroma.affymetrix,
   which happens when loading 'affyPLM', affy will overload
   the generic function plotDensity() with a regular function
   breaking that method in aroma.affymetrix. The solution
   is to make sure 'affy' is always loaded before, which was done
   by adding 'affy' to 'Depends:' in DESCRIPTION.  We have the
   same problem with the 'oligo' package, which is required by
   the CrlmmModel class.  However, for now, we leave that package
   under 'Suggests:'.


Version: 0.3.2 [2007-01-06]
  
 * Major changes.
  
 * Renamed all Preprocessing classes to Transform classes.
  
 * Introduced trial version of a top-level Model class in
   order to minimize repeated code.

DEPRECATED AND DEFUNCT:
  
 * Made several methods "private" in order to hide them
   form the HTML help tables.  Developers should rely on
   source code and Rdoc comments for now.


Version: 0.3.1 [2007-01-05]
  
 * Package pass R CMD check v2.4.0 (with one warning I suspect
   is a bug in R CMD check).
  
 * Some code was moved to 'affxparser' (v1.7.3) so it is
   recommended to update to that as soon as it is available
   on the Bioconductor servers.
  
 * Added initial code for PLASQ, but more is still needed.
  
 * In addition to default "PM only" model, ProbeLevelModel:s now
   also handles "PM-MM" models.  Note that PM-MM might give a
   non-positive value.  The multiplicate MbeiPlm handles this,
   but also the log-additive RmaPlm where such values become NAs.
 
 
Version: 0.3.0 [2006-12-20]
  
 * Made fitGlad() for classes CnChipEffectFile and CnChipEffectSet
   deprecated.  Use the GladModel class instead.
 
 
Version: 0.3.0 [2006-12-08]
  
 * Major updates. See below.
  
 * Change in directory structures.  Now all probe-level data
   is outputted to probeData/, and all PLM data to plmData/.
   Data from the GladModel is stored to gladData/.  Data sets
   with the same name processed in different ways will be
   distinguishable by their tags.
  
 * Pre-processing methods have now been split up in two major
   classes, the ProbePreprocessing and ChipEffectPreprocessing
   (both inheriting from the Preprocessing class) to indicate
   that they operate on probe-level and chip-effect data,
   respectively. All ProbePreprocessing classes output data
   to the probeData/ directory, and the ChipEffectPreprocessing
   class to the plmData/ directory.
  
 * ProbePreprocessing classes:
   QuantileNormalization replaces QuantileNormalizer.
   AlleleCrosstalkCalibration replaces AlleleCrosstalkCalibrator.
   PcrProbeCalibration corrects for PCR effects due to oligo
   sequence and SNP fragment lengths, cf. CRLMM.
   Adapted from oligo.
  
 * ChipEffectPreprocessing classes:
   FragmentLengthNormalization to normalize for PCR fragment-
   length effects after PLM, cf. CNAG.
  
 * Added the PlatformDesign class which provides an interface to
   a platform-design package without loading the package.  This
   is used for instance by the PcrProbeCalibration class.
 
 
Version: 0.2.6 [2006-12-07]
  
 * The recently added methods below makes it possible to store
   FeatureSet data to CEL files, which will further simplify
   bridging the aroma.affymetrix and the oligo package.
  
 * Added protected importFeatureSet() to import probe signals
   from a single-sample oligo::FeatureSet object.
  
 * Added static method createBlankSet() to AffymetrixCelSet
   to create a set of blank CEL files.
  
 * Added trial version of writeWig() to CnChipEffectSet to export
   log2 copy numbers to the UCSC Genome Browser.

BUG FIXES:
  
 * BUG FIX: The internal cache for readUnits() of ChipEffectFile
   classes was not sensitive to neither class nor parameters
   specific to subclasses.

 
Version: 0.2.5 [2006-11-22]
  
 * Package pass R CMD check.
  
 * Added GladModel.  Now it is fairly simple to estimate total
   copy numbers from Affymetrix 10K, 100K and 500K data sets.
  
 * Added support for tags to most classes.
  
 * Made encode() and decode() of ParameterCelFile approx 2-3 times
   faster by skipping the encode-/decodeUnit() step and instead
   call the encode and decode functions directly.  This will
   speed up the updating of chip-effect files about two times.
  
 * Added R.native to the list of suggested packages. The reason
   for this is that getAverageFile() of AffymetrixCelSet is
   using rowMedians(x, na.rm) of R.native.  The version in Biobase
   does not handle missing values.  In case R.native is not
   installed, apply() and median() are used.
  
 * Added SE estimates in RmaPlm from new affyPLM.
 
 
Version: 0.2.4 [2006-10-28]
  
 * Added more Rdoc comments.
 
 
Version: 0.2.3 [2006-10-23]
  
 * Added gcrma background correction.  Contributed by Ken Simpson,
   WEHI, Melbourne.
  
 * Added extractAffyBatch() to AffymetrixCelSet extracting data
   applicable to methods in the affy package.
  
 * Added extractSnpFeatureSet() to AffymetrixCelSet and
   extractSnpQSet() to SnpChipEffectSet extracting data applicable
   to methods in the oligo package.
  
 * Added trial versions of AffymetrixSnpCdfFile, GenotypeCallFile,
   GenotypeCallSet etc.
 
 
Version: 0.2.2 [2006-09-16]
  
 * Added basic support for dChip genome information.  It is good
   enough though to work with the 100K and 500K SNP chips.
  
 * Package now passes R CMD check.  Some cheating were done though,
   because methods with missing Rdoc where put as \alias{}:es in
   one place.
 
 
Version: 0.2.1 [2006-09-07]
  
 * Another big change in how classes are named.
 
 
Version: 0.2.0 [2006-08-25]
  
 * Have done a big redesign of the package. There are now also
   some basic model fitting algorithm available.  Probe-affinity
   estimates are stored in CEL files. Soon chip effects will also
   be stored in CEL files using customized CDF files that we very
   can write using the affxparser package.
 
 
Version: 0.1.5 [2006-07-2x]
  
 * BUG FIX: The 'outPath' argument of normalizeQuantile() in the
   AffymetrixDataset class was not recognized.
 
 
Version: 0.1.4 [2006-07-24]
  
 * Important breakthrough: We've update affxparser v1.5.3 with a working
   updateCel() function to update CEL v4 files.  This makes it possible
   to write normalized probe-level data as CEL files, e.g. now you can
   use normalizeQuantile(..., format="cel") to generate CEL files.  Note
   that this only works with binary CEL files (v4); ASCII CEL files (v3)
   and Calvin CEL files (upcoming binary format) is not supported.
  
 * Now findCdf() throws an exception if CDF file is not found.
 
 
Version: 0.1.3 [2006-07-05]
  
BUG FIXES:
  
 * BUG FIX/WORKAROUND: Currently the affxparser code crash R if the file
   is not a valid CEL file.  The best we can do now is to test that the
   filename has suffix *.CEL.  Thanks Ken Simpson, WEHI, Melbourne for
   pointing this out.
 
 
Version: 0.1.2 [2006-06-13]
  
 * Made the static fromFile() and fromFiles() methods more  generic such that
   it is easier to subset the different classes, e.g. for SNP chip classes.
 
 
Version: 0.1.1 [2006-05-30]
  
 * Cleaned up the API and the Rd help.
  
 * "Finalized" the quantile normalization.
 
 
Version: 0.1.0 [2006-01-11]
  
 * Created.
