Analysis of Large Affymetrix Microarray Data Sets

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Documentation for package ‘aroma.affymetrix’ version 3.0.0

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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 --

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