# Analysis of Large Affymetrix Microarray Data Sets

## Documentation for package ‘aroma.affymetrix’ version 3.2.2

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C D E F G H J L M N O P Q R S T U W

aroma.affymetrix-package | Package aroma.affymetrix

## -- A --

AbstractProbeSequenceNormalization | The AbstractProbeSequenceNormalization class
AdditiveCovariatesNormalization | The AdditiveCovariatesNormalization class
AffineCnPlm | The AffineCnPlm class
AffinePlm | The AffinePlm class
AffineSnpPlm | The AffineSnpPlm class
AffymetrixCdfFile | The AffymetrixCdfFile class
AffymetrixCelFile | The AffymetrixCelFile class
AffymetrixCelSet | The AffymetrixCelSet class
AffymetrixCelSetReporter | The AffymetrixCelSetReporter class
AffymetrixCelSetTuple | The AffymetrixCelSetTuple class
AffymetrixCnChpSet | The AffymetrixCnChpSet class
AffymetrixFile | The abstract AffymetrixFile class
AffymetrixFileSet | The AffymetrixFileSet class
AffymetrixFileSetReporter | The AffymetrixFileSetReporter class
AffymetrixPgfFile | The AffymetrixPgfFile class
AlleleSummation | The AlleleSummation class
AllelicCrosstalkCalibration | The AllelicCrosstalkCalibration class
aroma.affymetrix | Package aroma.affymetrix
AromaChipTypeAnnotationFile | The AromaChipTypeAnnotationFile class
ArrayExplorer | The ArrayExplorer class
AvgCnPlm | The AvgCnPlm class
AvgPlm | The AvgPlm class
AvgSnpPlm | The AvgSnpPlm class

## -- B --

BackgroundCorrection | The BackgroundCorrection class
BaseCountNormalization | The BaseCountNormalization class
BasePositionNormalization | The BasePositionNormalization class

## -- C --

ChipEffectFile | The ChipEffectFile class
ChipEffectSet | The ChipEffectSet class
ChipEffectTransform | The ChipEffectTransform class
CnagCfhFile | The CnagCfhFile class
CnagCfhSet | The CnagCfhSet class
CnChipEffectFile | The CnChipEffectFile class
CnChipEffectSet | The CnChipEffectSet class
CnPlm | The CnPlm class
CnProbeAffinityFile | The CnProbeAffinityFile class
CrlmmParametersFile | The CrlmmParametersFile class
CrlmmParametersSet | The CrlmmParametersSet class

## -- D --

DChipCdfBinFile | The DChipCdfBinFile class
DChipDcpFile | The DChipDcpFile class
DChipDcpSet | The DChipDcpSet class
DChipGenomeInformation | The DChipGenomeInformation class
DChipQuantileNormalization | The DChipQuantileNormalization class
DChipSnpInformation | The DChipSnpInformation class
doASCRMAv1 | Estimation and assessment of raw copy numbers at the single locus level (CRMA v1)
doASCRMAv1.default | Estimation and assessment of raw copy numbers at the single locus level (CRMA v1)
doASCRMAv2 | A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays (CRMA v2)
doASCRMAv2.default | A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays (CRMA v2)
doCRMAv1 | Estimation and assessment of raw copy numbers at the single locus level (CRMA v1)
doCRMAv1.AffymetrixCelSet | Estimation and assessment of raw copy numbers at the single locus level (CRMA v1)
doCRMAv1.default | Estimation and assessment of raw copy numbers at the single locus level (CRMA v1)
doCRMAv2 | A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays (CRMA v2)
doCRMAv2.AffymetrixCelSet | A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays (CRMA v2)
doCRMAv2.default | A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays (CRMA v2)
doFIRMA | Finding Isoforms using Robust Multichip Analysis (FIRMA)
doFIRMA.AffymetrixCelSet | Finding Isoforms using Robust Multichip Analysis (FIRMA)
doFIRMA.default | Finding Isoforms using Robust Multichip Analysis (FIRMA)
doGCRMA | Robust Multichip Analysis (GCRMA)
doGCRMA.AffymetrixCelSet | Robust Multichip Analysis (GCRMA)
doGCRMA.default | Robust Multichip Analysis (GCRMA)
doRMA | Robust Multichip Analysis (RMA)
doRMA.AffymetrixCelSet | Robust Multichip Analysis (RMA)
doRMA.default | Robust Multichip Analysis (RMA)

## -- E --

ExonChipEffectFile | The ExonChipEffectFile class
ExonChipEffectSet | The ExonChipEffectSet class
ExonProbeAffinityFile | The ExonProbeAffinityFile class
ExonRmaPlm | The ExonRmaPlm class

## -- F --

FirmaFile | The FirmaFile class
FirmaModel | The FirmaModel class
FirmaSet | The FirmaSet class
FragmentEquivalentClassNormalization | The FragmentEquivalentClassNormalization class
FragmentLengthNormalization | The FragmentLengthNormalization class

## -- G --

GcContentNormalization | The GcContentNormalization class
GcContentNormalization2 | The GcContentNormalization2 class
GcRmaBackgroundCorrection | The GcRmaBackgroundCorrection class
GenericReporter | The GenericReporter class
GenomeInformation | The GenomeInformation class

## -- H --

HetLogAddCnPlm | The HetLogAddCnPlm class
HetLogAddPlm | The HetLogAddPlm class
HetLogAddSnpPlm | The HetLogAddSnpPlm class

## -- J --

justRMA | Robust Multichip Analysis (RMA) reproducing the affy package
justRMA.AffymetrixCelSet | Robust Multichip Analysis (RMA) reproducing the affy package
justRMA.default | Robust Multichip Analysis (RMA) reproducing the affy package

## -- L --

LimmaBackgroundCorrection | The LimmaBackgroundCorrection class
LinearModelProbeSequenceNormalization | The LinearModelProbeSequenceNormalization class

## -- M --

MatNormalization | The MatNormalization class
MatSmoothing | The MatSmoothing class
MbeiCnPlm | The MbeiCnPlm class
MbeiPlm | The MbeiPlm class
MbeiSnpPlm | The MbeiSnpPlm class
Model | The Model class
MultiArrayUnitModel | The MultiArrayUnitModel class

## -- N --

nbrOfArrays.AffymetrixCelSet | The AffymetrixCelSet class
NormExpBackgroundCorrection | The NormExpBackgroundCorrection class

## -- O --

OpticalBackgroundCorrection | The OpticalBackgroundCorrection class

## -- P --

ParameterCelFile | The ParameterCelFile class
ParameterCelSet | The ParameterCelSet class
ProbeAffinityFile | The ProbeAffinityFile class
ProbeLevelModel | The ProbeLevelModel class
ProbeLevelTransform | The ProbeLevelTransform class
ProbeLevelTransform3 | The ProbeLevelTransform3 class

## -- Q --

QualityAssessmentFile | The QualityAssessmentFile class
QualityAssessmentModel | The QualityAssessmentModel class
QualityAssessmentSet | The QualityAssessmentSet class
QuantileNormalization | The QuantileNormalization class

## -- R --

ReseqCrosstalkCalibration | The ReseqCrosstalkCalibration class
ResidualFile | The ResidualFile class
ResidualSet | The ResidualSet class
RmaBackgroundCorrection | The RmaBackgroundCorrection class
RmaCnPlm | The RmaCnPlm class
RmaPlm | The RmaPlm class
RmaSnpPlm | The RmaSnpPlm class

## -- S --

ScaleNormalization | The ScaleNormalization class
ScaleNormalization3 | The ScaleNormalization3 class
SingleArrayUnitModel | The SingleArrayUnitModel class
SmoothMultiarrayModel | The SmoothMultiarrayModel class
SmoothRmaModel | The SmoothRmaModel class
SnpChipEffectFile | The SnpChipEffectFile class
SnpChipEffectSet | The SnpChipEffectSet class
SnpInformation | The SnpInformation class
SnpPlm | The SnpPlm interface class
SnpProbeAffinityFile | The SnpProbeAffinityFile class
SpatialReporter | The SpatialReporter class

## -- T --

TransformReport | The TransformReport class

## -- U --

UgpGenomeInformation | The UgpGenomeInformation class
UnitModel | The UnitModel class
UnitTypeScaleNormalization | The UnitTypeScaleNormalization class

## -- W --

WeightsFile | The WeightsFile class
WeightsSet | The WeightsSet class