Analysis of Large Affymetrix Microarray Data Sets

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Documentation for package ‘aroma.affymetrix’ version 3.2.2

• DESCRIPTION file.
• Package NEWS.

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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