API for aroma.affymetrix
Analysis of Large Affymetrix Microarray Data Sets

Global functions
.annotation	Source code
.applyCdfGroups	Source code
.assayData	Source code
.calibrateMultiscan	Source code
.cdfAddPlasqTypes	Source code
.cdfHeaderToCelHeader	Source code
.cleanPlatformName	Source code
.compareCdfs	Source code
.convertCdf	Source code
.convertCel	Source code
.createCel	Source code
.featureNames	Source code
.findCdf	Source code
.geometry	Source code
.getPlatformDesign	Source code
.invertMap	Source code
.normalizeFragmentLength	Source code
.normalizeQuantile	Source code
.normalizeQuantileSpline	Source code
.onAttach	Source code
.onLoad	Source code
.readBpmap	Source code
.readBpmapHeader	Source code
.readCcg	Source code
.readCcgHeader	Source code
.readCdf	Source code
.readCdfCellIndices	Source code
.readCdfGroupNames	Source code
.readCdfHeader	Source code
.readCdfIsPm	Source code
.readCdfNbrOfCellsPerUnitGroup	Source code
.readCdfQc	Source code
.readCdfUnitNames	Source code
.readCdfUnits	Source code
.readCel	Source code
.readCelHeader	Source code
.readCelRectangle	Source code
.readCelUnits	Source code
.readPgfEnv	Source code
.readPgfHeader	Source code
.robustSmoothSpline	Source code
.sampleNames	Source code
.setupAromaAffymetrix	Source code
.updateCel	Source code
.updateCelUnits	Source code
.writeCdf	Source code
.writeCdfHeader	Source code
.writeCdfQcUnits	Source code
.writeCdfUnits	Source code
ASCRMAv2	Man page
AbstractProbeSequenceNormalization	Man page
AbstractProbeSequenceNormalization.process	Man page
AdditiveCovariatesNormalization	Man page
AdditiveCovariatesNormalization.process	Man page
AffineCnPlm	Man page
AffinePlm	Man page
AffinePlm.getFitUnitGroupFunction	Man page
AffineSnpPlm	Man page
AffyGenePDInfo.writeCdf	Man page
AffymetrixAptSummaryFile	Man page
AffymetrixCdfFile	Man page
AffymetrixCdfFile$findByChipType	Man page
AffymetrixCdfFile$fromFile	Man page
AffymetrixCdfFile.compare	Man page
AffymetrixCdfFile.computeAffinities	Man page
AffymetrixCdfFile.convert	Man page
AffymetrixCdfFile.convertUnits	Man page
AffymetrixCdfFile.createExonByTranscriptCdf	Man page
AffymetrixCdfFile.createMonoCell	Man page
AffymetrixCdfFile.createMonocellCdf	Man page
AffymetrixCdfFile.createUnique	Man page
AffymetrixCdfFile.createUniqueCdf	Man page
AffymetrixCdfFile.findByChipType	Man page
AffymetrixCdfFile.fromFile	Man page
AffymetrixCdfFile.getAlleleCellPairs	Man page
AffymetrixCdfFile.getAlleleProbePairs	Man page
AffymetrixCdfFile.getAlleleProbePairs3	Man page
AffymetrixCdfFile.getCellIndices	Man page
AffymetrixCdfFile.getCnNames	Man page
AffymetrixCdfFile.getGenomeInformation	Man page
AffymetrixCdfFile.getHeader	Man page
AffymetrixCdfFile.getSnpNames	Man page
AffymetrixCdfFile.getUnitNames	Man page
AffymetrixCdfFile.getUnitTypes	Man page
AffymetrixCdfFile.groupUnitsByDimension	Man page
AffymetrixCdfFile.isPm	Man page
AffymetrixCdfFile.isResequenceChip	Man page
AffymetrixCdfFile.isSnpChip	Man page
AffymetrixCdfFile.nbrOfGroupsPerUnit	Man page
AffymetrixCdfFile.nbrOfSnps	Man page
AffymetrixCdfFile.readUnits	Man page
AffymetrixCdfFile.readUnitsByQuartets	Man page
AffymetrixCdfFile.setRestructor	Man page
AffymetrixCelFile	Man page
AffymetrixCelFile$allocateFromCdf	Man page
AffymetrixCelFile$clearData	Man page
AffymetrixCelFile$fromFile	Man page
AffymetrixCelFile.allocateFromCdf	Man page
AffymetrixCelFile.clearData	Man page
AffymetrixCelFile.createFrom	Man page
AffymetrixCelFile.fitQuantileNormFcn	Man page
AffymetrixCelFile.fromFile	Man page
AffymetrixCelFile.getCdf	Man page
AffymetrixCelFile.getChipType	Man page
AffymetrixCelFile.getData	Man page
AffymetrixCelFile.getHeader	Man page
AffymetrixCelFile.getImage	Man page
AffymetrixCelFile.getTimestamp	Man page
AffymetrixCelFile.image270	Man page
AffymetrixCelFile.normalizeQuantile	Man page
AffymetrixCelFile.plotDensity	Man page
AffymetrixCelFile.plotImage	Man page
AffymetrixCelFile.plotMvsA	Man page
AffymetrixCelFile.plotMvsX	Man page
AffymetrixCelFile.readRawData	Man page
AffymetrixCelFile.readUnits	Man page
AffymetrixCelFile.setCdf	Man page
AffymetrixCelFile.smoothScatterMvsA	Man page
AffymetrixCelFile.updateUnits	Man page
AffymetrixCelFile.writeImage	Man page
AffymetrixCelSet	Man page
AffymetrixCelSet$importFromDChip	Man page
AffymetrixCelSet.as.AffymetrixCelSet	Man page
AffymetrixCelSet.as.character	Man page
AffymetrixCelSet.averageQuantile	Man page
AffymetrixCelSet.calculateParametersGsb	Man page
AffymetrixCelSet.extractAffyBatch	Man page
AffymetrixCelSet.extractFeatureSet	Man page
AffymetrixCelSet.extractMatrix	Man page
AffymetrixCelSet.extractSnpFeatureSet	Man page
AffymetrixCelSet.getAverageFile	Man page
AffymetrixCelSet.getCdf	Man page
AffymetrixCelSet.getChipType	Man page
AffymetrixCelSet.getIntensities	Man page
AffymetrixCelSet.getUnitIntensities	Man page
AffymetrixCelSet.importFromDChip	Man page
AffymetrixCelSet.isDuplicated	Man page
AffymetrixCelSet.normalizeQuantile	Man page
AffymetrixCelSet.plotDensity	Man page
AffymetrixCelSet.setCdf	Man page
AffymetrixCelSetReporter	Man page
AffymetrixCelSetReporter.getDataSet	Man page
AffymetrixCelSetTuple	Man page
AffymetrixCnChpFile	Man page
AffymetrixCnChpSet	Man page
AffymetrixCnChpSet.as.AffymetrixCnChpSet	Man page
AffymetrixCnChpSet.as.character	Man page
AffymetrixCsvFile	Man page
AffymetrixCsvGenomeInformation	Man page
AffymetrixFile	Man page
AffymetrixFileSet	Man page
AffymetrixFileSet$byPath	Man page
AffymetrixFileSet.as.AffymetrixFileSet	Man page
AffymetrixFileSet.byPath	Man page
AffymetrixFileSetReporter	Man page
AffymetrixNetAffxCsvFile	Man page
AffymetrixPgfFile	Man page
AffymetrixPgfFile$findByChipType	Man page
AffymetrixPgfFile$fromFile	Man page
AffymetrixPgfFile.findByChipType	Man page
AffymetrixPgfFile.fromFile	Man page
AffymetrixPgfFile.getHeader	Man page
AffymetrixPgfFile.getUnitNames	Man page
AffymetrixPlatform	Man page
AffymetrixProbeTabFile	Man page
AffymetrixTabularFile	Man page
AffymetrixTsvFile	Man page
AlleleSummation	Man page
AlleleSummation.getChipEffectSet	Man page
AllelicCrosstalkCalibration	Man page
AllelicCrosstalkCalibration.process	Man page
AromaAffymetrix	Man page
AromaAffymetrix.setupExampleData	Man page
AromaCellMatchScoreFile	Man page
AromaChipTypeAnnotationFile	Man page
AromaChipTypeAnnotationFile$byChipType	Man page
AromaChipTypeAnnotationFile$fromFile	Man page
AromaChipTypeAnnotationFile.byChipType	Man page
AromaChipTypeAnnotationFile.byName	Man page
AromaChipTypeAnnotationFile.findByChipType	Man page
AromaChipTypeAnnotationFile.fromFile	Man page
AromaChipTypeAnnotationFile.getHeader	Man page
AromaPipeline	Man page
AromaUfcFile	Man page
AromaUnitTabularBinaryFile$allocateFromCdf	Man page
AromaUnitTabularBinaryFile.allocateFromCdf	Man page
ArrayExplorer	Man page
ArrayExplorer.getDataSet	Man page
ArrayExplorer.process	Man page
ArrayExplorer.setArrays	Man page
AvgCnPlm	Man page
AvgPlm	Man page
AvgPlm.getFitUnitGroupFunction	Man page
AvgSnpPlm	Man page
BackgroundCorrection	Man page
BackgroundCorrection.process	Man page
BaseCountNormalization	Man page
BasePositionNormalization	Man page
ChipEffectFile	Man page
ChipEffectFile$fromDataFile	Man page
ChipEffectFile.fromDataFile	Man page
ChipEffectFile.getAM	Man page
ChipEffectFile.getCellIndices	Man page
ChipEffectFile.getCellMap	Man page
ChipEffectFile.getUnitGroupCellMap	Man page
ChipEffectFile.getXAM	Man page
ChipEffectGroupMerge	Man page
ChipEffectGroupMerge.process	Man page
ChipEffectSet	Man page
ChipEffectSet.calculateBaseline	Man page
ChipEffectSet.extractExpressionSet	Man page
ChipEffectSet.getAM	Man page
ChipEffectSet.getBaseline	Man page
ChipEffectSet.getXAM	Man page
ChipEffectSetTuple	Man page
ChipEffectTransform	Man page
CnChipEffectFile	Man page
CnChipEffectFile.getCellIndices	Man page
CnChipEffectSet	Man page
CnChipEffectSet$importFromApt	Man page
CnChipEffectSet$importFromDChip	Man page
CnChipEffectSet.importFromApt	Man page
CnChipEffectSet.importFromDChip	Man page
CnChipEffectSetTuple	Man page
CnPlm	Man page
CnProbeAffinityFile	Man page
CnProbeAffinityFile.getCellIndices	Man page
CnagCfhFile	Man page
CnagCfhFile$fromFile	Man page
CnagCfhFile.fromFile	Man page
CnagCfhFile.getCdf	Man page
CnagCfhFile.getChipType	Man page
CnagCfhFile.getHeader	Man page
CnagCfhFile.readUnits	Man page
CnagCfhFile.setCdf	Man page
CnagCfhSet	Man page
CnagCfhSet.as.CnagCfhSet	Man page
CnagCfhSet.as.character	Man page
CnagCfhSet.getAverageFile	Man page
CnagCfhSet.getCdf	Man page
CnagCfhSet.isDuplicated	Man page
CnagCfhSet.setCdf	Man page
CrlmmModel	Man page
CrlmmParametersFile	Man page
CrlmmParametersSet	Man page
DChipCdfBinFile	Man page
DChipDcpFile	Man page
DChipDcpSet	Man page
DChipDcpSet.as.DChipDcpSet	Man page
DChipDcpSet.as.character	Man page
DChipGenomeInformation	Man page
DChipGenomeInformation.byChipType	Man page
DChipQuantileNormalization	Man page
DChipQuantileNormalization.process	Man page
DChipSnpInformation	Man page
DChipSnpInformation.byChipType	Man page
Env2Cdf	Man page
ExonChipEffectFile	Man page
ExonChipEffectFile.getCellIndices	Man page
ExonChipEffectSet	Man page
ExonProbeAffinityFile	Man page
ExonProbeAffinityFile.getCellIndices	Man page
ExonRmaPlm	Man page
ExonRmaPlm.getFitUnitGroupFunction	Man page
FirmaFile	Man page
FirmaFile.getCellIndices	Man page
FirmaModel	Man page
FirmaModel.calculateResidualSet	Man page
FirmaModel.calculateResiduals	Man page
FirmaModel.findUnitsTodo	Man page
FirmaModel.fit	Man page
FirmaModel.getFirmaScores	Man page
FirmaModel.getFirmaSet	Man page
FirmaModel.getFitUnitGroupFunction	Man page
FirmaSet	Man page
FragmentEquivalentClassNormalization	Man page
FragmentEquivalentClassNormalization.process	Man page
FragmentLengthNormalization	Man page
FragmentLengthNormalization.process	Man page
GcContentNormalization	Man page
GcContentNormalization.process	Man page
GcContentNormalization2	Man page
GcRmaBackgroundCorrection	Man page
GcRmaBackgroundCorrection.process	Man page
GenericReporter	Man page
GenericReporter.getAlias	Man page
GenericReporter.getName	Man page
GenericReporter.getTags	Man page
GenericReporter.process	Man page
GenericReporter.setAlias	Man page
GenomeInformation	Man page
GenomeInformation$byChipType	Man page
GenomeInformation$fromCdf	Man page
GenomeInformation.byChipType	Man page
GenomeInformation.fromCdf	Man page
GenomeInformation.getChipType	Man page
GenomeInformation.getData	Man page
GenomeInformation.getPositions	Man page
GenomeInformation.getUnitIndices	Man page
GenomeInformation.plotDensity	Man page
GenomeInformation.verify	Man page
HetLogAddCnPlm	Man page
HetLogAddPlm	Man page
HetLogAddPlm.getFitUnitGroupFunction	Man page
HetLogAddSnpPlm	Man page
LimmaBackgroundCorrection	Man page
LimmaBackgroundCorrection.process	Man page
LinearModelProbeSequenceNormalization	Man page
MatNormalization	Man page
MatNormalization.process	Man page
MatSmoothing	Man page
MatSmoothing.process	Man page
MbeiCnPlm	Man page
MbeiPlm	Man page
MbeiPlm.getFitUnitGroupFunction	Man page
MbeiSnpPlm	Man page
Model	Man page
Model.fit	Man page
Model.getAlias	Man page
Model.getCdf	Man page
Model.getDataSet	Man page
Model.getFullName	Man page
Model.getName	Man page
Model.getPath	Man page
Model.getRootPath	Man page
Model.getTags	Man page
Model.setAlias	Man page
Model.setTags	Man page
MultiArrayUnitModel	Man page
MultiArrayUnitModel$getFitUnitGroupFunction	Man page
MultiArrayUnitModel.getFitUnitGroupFunction	Man page
MultiArrayUnitModel.readUnits	Man page
Non-documented objects	Man page
NormExpBackgroundCorrection	Man page
OpticalBackgroundCorrection	Man page
OpticalBackgroundCorrection.process	Man page
ParameterCelFile	Man page
ParameterCelSet	Man page
ParameterCelSet.extractDataFrame	Man page
ParameterCelSet.extractMatrix	Man page
ProbeAffinityFile	Man page
ProbeAffinityFile.getCellIndices	Man page
ProbeLevelModel	Man page
ProbeLevelModel.findUnitsTodo	Man page
ProbeLevelModel.fit	Man page
ProbeLevelModel.getChipEffectSet	Man page
ProbeLevelModel.getChipEffects	Man page
ProbeLevelModel.getProbeAffinities	Man page
ProbeLevelModel.getProbeAffinityFile	Man page
ProbeLevelTransform	Man page
ProbeLevelTransform3	Man page
QualityAssessmentFile	Man page
QualityAssessmentModel	Man page
QualityAssessmentModel.getResiduals	Man page
QualityAssessmentModel.getWeights	Man page
QualityAssessmentSet	Man page
QuantileNormalization	Man page
QuantileNormalization.process	Man page
ReseqCrosstalkCalibration	Man page
ReseqCrosstalkCalibration.process	Man page
ResidualFile	Man page
ResidualFile.getCellIndices	Man page
ResidualSet	Man page
RmaBackgroundCorrection	Man page
RmaBackgroundCorrection.process	Man page
RmaCnPlm	Man page
RmaPlm	Man page
RmaPlm.getFitUnitGroupFunction	Man page
RmaSnpPlm	Man page
ScaleNormalization	Man page
ScaleNormalization.process	Man page
ScaleNormalization3	Man page
ScaleNormalization3.process	Man page
SingleArrayUnitModel	Man page
SingleArrayUnitModel$getFitUnitGroupFunction	Man page
SingleArrayUnitModel.fit	Man page
SingleArrayUnitModel.getFitUnitGroupFunction	Man page
SingleArrayUnitModel.readUnits	Man page
SmoothMultiarrayModel	Man page
SmoothMultiarrayModel.fit	Man page
SmoothRmaModel	Man page
SmoothSaModel	Man page
SnpChipEffectFile	Man page
SnpChipEffectFile.getCellIndices	Man page
SnpChipEffectGroupMerge	Man page
SnpChipEffectSet	Man page
SnpInformation	Man page
SnpInformation$fromCdf	Man page
SnpInformation.byChipType	Man page
SnpInformation.fromCdf	Man page
SnpInformation.getChipType	Man page
SnpInformation.getData	Man page
SnpInformation.verify	Man page
SnpPlm	Man page
SnpProbeAffinityFile	Man page
SnpProbeAffinityFile.getCellIndices	Man page
SpatialReporter	Man page
SpatialReporter.process	Man page
SpatialRowColumnNormalization	Man page
Transform	Man page
Transform.getOutputDataSet	Man page
TransformReport	Man page
TransformReport.getFullName	Man page
TransformReport.getInputDataSet	Man page
TransformReport.getName	Man page
TransformReport.getOutputDataSet	Man page
TransformReport.getPath	Man page
TransformReport.getTags	Man page
UflSnpInformation	Man page
UgpGenomeInformation	Man page
UgpGenomeInformation$byChipType	Man page
UgpGenomeInformation.byChipType	Man page
UnitModel	Man page
UnitModel.findUnitsTodo	Man page
UnitModel.getCellIndices	Man page
UnitTypeScaleNormalization	Man page
UnitTypeScaleNormalization.process	Man page
WeightsFile	Man page
WeightsFile.getCellIndices	Man page
WeightsSet	Man page
`.annotation<-`	Source code
`.assayData<-`	Source code
`.featureNames<-`	Source code
`.phenoData<-`	Source code
`.protocolData<-`	Source code
`.sampleNames<-`	Source code
addColorMap	Man page
addColorMap.ArrayExplorer	Man page
addColorMap.SpatialReporter	Man page
addExclCells	Man page
addExclCells.DChipQuantileNormalization	Man page
allocate.AromaCellMatchScoreFile	Man page
allocate.CrlmmParametersFile	Man page
allocateFromCdf	Man page
allocateFromCdf,AffymetrixCelFile-method	Man page
allocateFromCdf,AromaUnitTabularBinaryFile-method	Man page
allocateFromCdf.AffymetrixCelFile	Man page
allocateFromCdf.AromaCellCpgFile	Man page
allocateFromCdf.AromaCellMatchScoreFile	Man page
allocateFromCdf.AromaCellPositionFile	Man page
allocateFromCdf.AromaCellSequenceFile	Man page
allocateFromCdf.AromaUfcFile	Man page
allocateFromCdf.AromaUflFile	Man page
allocateFromCdf.AromaUnitGcContentFile	Man page
allocateFromCdf.AromaUnitTabularBinaryFile	Man page
annotateMvsA	Man page
annotateMvsA.AffymetrixCelFile	Man page
append.AffymetrixCelSet	Man page
append.CnagCfhSet	Man page
applyAnyOrder	Man page
applyAnyOrder.CopyNumberChromosomalModel	Man page
applyCCF0	Man page
applyCCF0.CopyNumberChromosomalModel	Man page
applyCFC0	Man page
applyCFC0.CopyNumberChromosomalModel	Man page
applyToUnitIntensities	Man page
applyToUnitIntensities.AffymetrixCelSet	Man page
aroma.affymetrix	Man page
aroma.affymetrix-package	Man page
as.AffymetrixCelSet	Man page
as.AffymetrixCelSet,AffymetrixCelSet-method	Man page
as.AffymetrixCelSet.AffymetrixCelSet	Man page
as.AffymetrixCelSet.default	Man page
as.AffymetrixCelSet.list	Man page
as.AffymetrixCnChpSet	Man page
as.AffymetrixCnChpSet,AffymetrixCnChpSet-method	Man page
as.AffymetrixCnChpSet.AffymetrixCnChpSet	Man page
as.AffymetrixCnChpSet.default	Man page
as.AffymetrixCnChpSet.list	Man page
as.AffymetrixFileSet	Man page
as.AffymetrixFileSet,AffymetrixFileSet-method	Man page
as.AffymetrixFileSet.AffymetrixFileSet	Man page
as.AffymetrixFileSet.default	Man page
as.AffymetrixFileSet.list	Man page
as.ChipEffectSetTuple	Man page
as.ChipEffectSetTuple.ChipEffectSetTuple	Man page
as.ChipEffectSetTuple.default	Man page
as.CnChipEffectSetTuple	Man page
as.CnChipEffectSetTuple.CnChipEffectSetTuple	Man page
as.CnChipEffectSetTuple.default	Man page
as.CnagCfhSet	Man page
as.CnagCfhSet,CnagCfhSet-method	Man page
as.CnagCfhSet.CnagCfhSet	Man page
as.CnagCfhSet.default	Man page
as.CnagCfhSet.list	Man page
as.CopyNumberDataSetTuple.CnChipEffectSet	Man page
as.DChipDcpSet	Man page
as.DChipDcpSet,DChipDcpSet-method	Man page
as.DChipDcpSet.DChipDcpSet	Man page
as.DChipDcpSet.default	Man page
as.DChipDcpSet.list	Man page
as.character,AffymetrixCelSet-method	Man page
as.character,AffymetrixCnChpSet-method	Man page
as.character,CnagCfhSet-method	Man page
as.character,DChipDcpSet-method	Man page
as.character.AffymetrixCdfFile	Man page
as.character.AffymetrixCelFile	Man page
as.character.AffymetrixCelSet	Man page
as.character.AffymetrixCelSetReporter	Man page
as.character.AffymetrixCnChpFile	Man page
as.character.AffymetrixCnChpSet	Man page
as.character.AffymetrixPgfFile	Man page
as.character.AffymetrixProbeTabFile	Man page
as.character.AromaChipTypeAnnotationFile	Man page
as.character.ArrayExplorer	Man page
as.character.ChipEffectFile	Man page
as.character.ChipEffectSet	Man page
as.character.CnagCfhFile	Man page
as.character.CnagCfhSet	Man page
as.character.DChipCdfBinFile	Man page
as.character.DChipDcpFile	Man page
as.character.DChipDcpSet	Man page
as.character.DChipQuantileNormalization	Man page
as.character.FirmaModel	Man page
as.character.GenericReporter	Man page
as.character.GenomeInformation	Man page
as.character.Model	Man page
as.character.ProbeAffinityFile	Man page
as.character.QualityAssessmentModel	Man page
as.character.ResidualFile	Man page
as.character.ResidualSet	Man page
as.character.SmoothMultiarrayModel	Man page
as.character.SnpInformation	Man page
as.character.SpatialReporter	Man page
as.character.TransformReport	Man page
as.character.WeightsFile	Man page
as.character.WeightsSet	Man page
assertAnnotationData	Man page
assertAnnotationData.ASCRMAv2	Man page
averageQuantile	Man page
averageQuantile,AffymetrixCelSet-method	Man page
averageQuantile.AffymetrixCelSet	Man page
bgAdjustGcrma	Man page
bgAdjustOptical	Man page
bgAdjustRma	Man page
boxplotStats	Man page
boxplotStats.ChipEffectSet	Man page
bpmapCluster2Cdf	Man page
bpmapCluster2Cdf.default	Man page
byChipType,AromaChipTypeAnnotationFile-method	Man page
byChipType,DChipGenomeInformation-method	Man page
byChipType,DChipSnpInformation-method	Man page
byChipType,GenomeInformation-method	Man page
byChipType,SnpInformation-method	Man page
byChipType,UgpGenomeInformation-method	Man page
byChipType.AffymetrixCsvGenomeInformation	Man page
byChipType.AffymetrixProbeTabFile	Man page
byChipType.AffymetrixTabularFile	Man page
byChipType.AffymetrixTsvFile	Man page
byChipType.AromaCellMatchScoreFile	Man page
byChipType.AromaChipTypeAnnotationFile	Man page
byChipType.DChipCdfBinFile	Man page
byChipType.DChipGenomeInformation	Man page
byChipType.DChipSnpInformation	Man page
byChipType.GenomeInformation	Man page
byChipType.SnpInformation	Man page
byChipType.UflSnpInformation	Man page
byChipType.UgpGenomeInformation	Man page
byName,AromaChipTypeAnnotationFile-method	Man page
byName.AffymetrixCelSet	Man page
byName.AffymetrixCnChpSet	Man page
byName.AromaChipTypeAnnotationFile	Man page
byName.CnagCfhSet	Man page
byName.CrlmmParametersSet	Man page
byName.DChipDcpSet	Man page
byPath,AffymetrixFileSet-method	Man page
byPath.AffymetrixCelSet	Man page
byPath.AffymetrixCelSetTuple	Man page
byPath.AffymetrixCnChpSet	Man page
byPath.AffymetrixFileSet	Man page
byPath.ChipEffectSet	Man page
byPath.CnChipEffectSet	Man page
byPath.CnagCfhSet	Man page
byPath.CrlmmParametersSet	Man page
byPath.DChipDcpSet	Man page
byPath.ExonChipEffectSet	Man page
byPath.FirmaSet	Man page
byPath.ResidualSet	Man page
byPath.SnpChipEffectSet	Man page
byPath.WeightsSet	Man page
calcRawCnStats	Man page
calcRawCnStats.CopyNumberChromosomalModel	Man page
calcRawCnStats.default	Man page
calculateAffinities	Man page
calculateAffinities.GcRmaBackgroundCorrection	Man page
calculateAverages	Man page
calculateAverages.FragmentEquivalentClassNormalization	Man page
calculateBaseline	Man page
calculateBaseline,ChipEffectSet-method	Man page
calculateBaseline.ChipEffectSet	Man page
calculateConfidenceScores	Man page
calculateConfidenceScores.CrlmmModel	Man page
calculateFieldBoxplotStats	Man page
calculateFieldBoxplotStats.ChipEffectSet	Man page
calculateMargins	Man page
calculateMargins.SpatialReporter	Man page
calculateNuseBoxplotStats	Man page
calculateNuseBoxplotStats.ChipEffectSet	Man page
calculateParametersGsb	Man page
calculateParametersGsb,AffymetrixCelSet-method	Man page
calculateParametersGsb.AffymetrixCelSet	Man page
calculateResidualSet	Man page
calculateResidualSet,FirmaModel-method	Man page
calculateResidualSet.FirmaModel	Man page
calculateResidualSet.ProbeLevelModel	Man page
calculateResiduals,FirmaModel-method	Man page
calculateResiduals.FirmaModel	Man page
calculateRleBoxplotStats	Man page
calculateRleBoxplotStats.ChipEffectSet	Man page
calculateTargetDistribution	Man page
calculateTargetDistribution.QuantileNormalization	Man page
calculateWeights	Man page
calculateWeights.ExonRmaPlm	Man page
calculateWeights.FirmaModel	Man page
calculateWeights.ProbeLevelModel	Man page
calibrateOne	Man page
calibrateOne.ReseqCrosstalkCalibration	Man page
cdfMergeGroups	Man page Source code
clearCache.AffymetrixCelSet	Man page
clearData	Man page
clearData,AffymetrixCelFile-method	Man page
clearData.AffymetrixCelFile	Man page
clone.AffymetrixCelFile	Man page
clone.AffymetrixCelSet	Man page
clone.AffymetrixCnChpFile	Man page
clone.CnagCfhFile	Man page
clone.CnagCfhSet	Man page
compare	Man page
compare,AffymetrixCdfFile-method	Man page
compare.AffymetrixCdfFile	Man page
computeAffinities	Man page
computeAffinities,AffymetrixCdfFile-method	Man page
computeAffinities.AffymetrixCdfFile	Man page
computeAffinitiesByACS	Man page
computeAffinitiesByACS.AffymetrixCdfFile	Man page
convert	Man page
convert,AffymetrixCdfFile-method	Man page
convert.AffymetrixCdfFile	Man page
convertToUnique	Man page
convertToUnique.AffymetrixCelSet	Man page
convertUnits	Man page
convertUnits,AffymetrixCdfFile-method	Man page
convertUnits.AffymetrixCdfFile	Man page
createExonByTranscriptCdf	Man page
createExonByTranscriptCdf,AffymetrixCdfFile-method	Man page
createExonByTranscriptCdf.AffymetrixCdfFile	Man page
createFrom	Man page
createFrom,AffymetrixCelFile-method	Man page
createFrom.AffymetrixCelFile	Man page
createMonoCell,AffymetrixCdfFile-method	Man page
createMonoCell.AffymetrixCdfFile	Man page
createMonocellCdf	Man page
createMonocellCdf,AffymetrixCdfFile-method	Man page
createMonocellCdf.AffymetrixCdfFile	Man page
createOutputTuple	Man page
createOutputTuple.SmoothMultiarrayModel	Man page
createParamCdf	Man page
createParamCdf.ChipEffectFile	Man page
createParamCdf.FirmaFile	Man page
createUnique,AffymetrixCdfFile-method	Man page
createUnique.AffymetrixCdfFile	Man page
createUniqueCdf	Man page
createUniqueCdf,AffymetrixCdfFile-method	Man page
createUniqueCdf.AffymetrixCdfFile	Man page
decode	Man page
decode.ParameterCelFile	Man page
dim.DChipDcpFile	Man page
doASCRMAv1	Man page
doASCRMAv1.default	Man page
doASCRMAv2	Man page
doASCRMAv2.default	Man page
doCRMAv1	Man page
doCRMAv1.AffymetrixCelSet	Man page
doCRMAv1.default	Man page
doCRMAv2	Man page
doCRMAv2.AffymetrixCelSet	Man page
doCRMAv2.default	Man page
doFIRMA	Man page
doFIRMA.AffymetrixCelSet	Man page
doFIRMA.default	Man page
doGCRMA	Man page
doGCRMA.AffymetrixCelSet	Man page
doGCRMA.default	Man page
doRMA	Man page
doRMA.AffymetrixCelSet	Man page
doRMA.default	Man page
dropCellsFromCdfList	Man page Source code
encode	Man page
encode.ParameterCelFile	Man page
env2Cdf	Man page Source code
excludeChrXFromFit	Man page
excludeChrXFromFit.DChipQuantileNormalization	Man page
exportAromaSignalBinaryFileList	Man page
exportAromaSignalBinaryFileList.CnChipEffectFile	Man page
exportTotalAndFracB	Man page
exportTotalAndFracB.CnChipEffectFile	Man page
exportTotalAndFracB.CnChipEffectSet	Man page
exportTotalAndFracB.DChipDcpSet	Man page
exportTotalAndFracB.SnpChipEffectFile	Man page
exportTotalAndFracB.SnpChipEffectSet	Man page
exportTotalCnRatioSet.AffymetrixCnChpSet	Man page
extractAffyBatch	Man page
extractAffyBatch,AffymetrixCelSet-method	Man page
extractAffyBatch.AffymetrixCelSet	Man page
extractAffyBatch.ChipEffectSet	Man page
extractAlleleSet	Man page
extractAlleleSet.SnpChipEffectSet	Man page
extractCNT	Man page
extractCNT.SnpChipEffectFile	Man page
extractCNT.SnpChipEffectSet	Man page
extractChromosomalDataFrame	Man page
extractChromosomalDataFrame.ChipEffectFile	Man page
extractChromosomalDataFrame.ChipEffectSet	Man page
extractDataFrame	Man page
extractDataFrame,ParameterCelSet-method	Man page
extractDataFrame.ParameterCelFile	Man page
extractDataFrame.ParameterCelSet	Man page
extractExpressionSet	Man page
extractExpressionSet,ChipEffectSet-method	Man page
extractExpressionSet.ChipEffectSet	Man page
extractFeatureSet	Man page
extractFeatureSet,AffymetrixCelSet-method	Man page
extractFeatureSet.AffymetrixCelSet	Man page
extractLogRatios	Man page
extractLogRatios.AffymetrixCnChpFile	Man page
extractLogRatios.AffymetrixCnChpSet	Man page
extractMatrix,AffymetrixCelSet-method	Man page
extractMatrix,ParameterCelSet-method	Man page
extractMatrix.AffymetrixCelFile	Man page
extractMatrix.AffymetrixCelSet	Man page
extractMatrix.ChipEffectFile	Man page
extractMatrix.ChipEffectSet	Man page
extractMatrix.FirmaFile	Man page
extractMatrix.FirmaSet	Man page
extractMatrix.ParameterCelFile	Man page
extractMatrix.ParameterCelSet	Man page
extractSnpCnvQSet	Man page
extractSnpCnvQSet.SnpChipEffectSet	Man page
extractSnpFeatureSet	Man page
extractSnpFeatureSet,AffymetrixCelSet-method	Man page
extractSnpFeatureSet.AffymetrixCelSet	Man page
extractSnpQSet	Man page
extractSnpQSet.SnpChipEffectSet	Man page
extractTheta	Man page
extractTheta.ChipEffectFile	Man page
extractTheta.ChipEffectSet	Man page
extractTheta.CnChipEffectFile	Man page
extractTheta.CnChipEffectSet	Man page
extractTheta.DChipDcpFile	Man page
extractTheta.DChipDcpSet	Man page
extractTheta.SnpChipEffectFile	Man page
extractTheta.SnpChipEffectSet	Man page
extractTheta.SnpCnvQSet	Man page
extractTheta.SnpQSet	Man page
extractTotalAndFracB	Man page
extractTotalAndFracB.SnpChipEffectFile	Man page
extractTotalAndFreqB	Man page
extractTotalAndFreqB.CnChipEffectFile	Man page
extractTotalAndFreqB.CnChipEffectSet	Man page
extractTotalAndFreqB.SnpChipEffectSet	Man page
extractTotalAndFreqB.default	Man page
findByCdf2	Man page
findByCdf2.default	Man page
findByChipType,AffymetrixCdfFile-method	Man page
findByChipType,AffymetrixPgfFile-method	Man page
findByChipType,AromaChipTypeAnnotationFile-method	Man page
findByChipType.AffymetrixCdfFile	Man page
findByChipType.AffymetrixCsvFile	Man page
findByChipType.AffymetrixCsvGenomeInformation	Man page
findByChipType.AffymetrixNetAffxCsvFile	Man page
findByChipType.AffymetrixPgfFile	Man page
findByChipType.AffymetrixProbeTabFile	Man page
findByChipType.AffymetrixTabularFile	Man page
findByChipType.AffymetrixTsvFile	Man page
findByChipType.AromaChipTypeAnnotationFile	Man page
findByChipType.DChipCdfBinFile	Man page
findByChipType.DChipGenomeInformation	Man page
findByChipType.DChipSnpInformation	Man page
findByChipType.UflSnpInformation	Man page
findByChipType.UgpGenomeInformation	Man page
findByName.AffymetrixCelSet	Man page
findByName.AffymetrixCnChpSet	Man page
findByName.ChipEffectSet	Man page
findByName.CnagCfhSet	Man page
findByName.DChipDcpSet	Man page
findTargetDistributionFile	Man page
findTargetDistributionFile.QuantileNormalization	Man page
findUnitsTodo,FirmaModel-method	Man page
findUnitsTodo,ProbeLevelModel-method	Man page
findUnitsTodo,UnitModel-method	Man page
findUnitsTodo.AlleleSummation	Man page
findUnitsTodo.ChipEffectFile	Man page
findUnitsTodo.ChipEffectSet	Man page
findUnitsTodo.CrlmmModel	Man page
findUnitsTodo.CrlmmParametersFile	Man page
findUnitsTodo.CrlmmParametersSet	Man page
findUnitsTodo.ExonChipEffectSet	Man page
findUnitsTodo.FirmaFile	Man page
findUnitsTodo.FirmaModel	Man page
findUnitsTodo.FirmaSet	Man page
findUnitsTodo.ProbeLevelModel	Man page
findUnitsTodo.QualityAssessmentFile	Man page
findUnitsTodo.ResidualFile	Man page
findUnitsTodo.ResidualSet	Man page
findUnitsTodo.UnitModel	Man page
findUnitsTodo.WeightsFile	Man page
findUnitsTodo.WeightsSet	Man page
fit,FirmaModel-method	Man page
fit,Model-method	Man page
fit,ProbeLevelModel-method	Man page
fit,SingleArrayUnitModel-method	Man page
fit,SmoothMultiarrayModel-method	Man page
fit.CrlmmModel	Man page
fit.FirmaModel	Man page
fit.Model	Man page
fit.ProbeLevelModel	Man page
fit.SingleArrayUnitModel	Man page
fit.SmoothMultiarrayModel	Man page
fitCnProbes	Man page
fitCnProbes.UnitModel	Man page
fitOne	Man page
fitOne.AbstractProbeSequenceNormalization	Man page
fitOne.BaseCountNormalization	Man page
fitOne.LinearModelProbeSequenceNormalization	Man page
fitOne.MatNormalization	Man page
fitOne.ReseqCrosstalkCalibration	Man page
fitOne.ScaleNormalization3	Man page
fitOne.UnitTypeScaleNormalization	Man page
fitOneArray	Man page
fitOneArray.SingleArrayUnitModel	Man page
fitOneChromosome	Man page
fitOneChromosome.SmoothMultiarrayModel	Man page
fitPlasqUnit	Man page
fitPlasqUnit.matrix	Man page
fitQuantileNormFcn	Man page
fitQuantileNormFcn,AffymetrixCelFile-method	Man page
fitQuantileNormFcn.AffymetrixCelFile	Man page
fixSearchPath.AromaAffymetrix	Man page
fromCdf	Man page
fromCdf,GenomeInformation-method	Man page
fromCdf,SnpInformation-method	Man page
fromCdf.AffymetrixProbeTabFile	Man page
fromCdf.GenomeInformation	Man page
fromCdf.SnpInformation	Man page
fromDataFile	Man page
fromDataFile,ChipEffectFile-method	Man page
fromDataFile.ChipEffectFile	Man page
fromDataFile.FirmaFile	Man page
fromDataFile.ResidualFile	Man page
fromDataFile.WeightsFile	Man page
fromDataSet	Man page
fromDataSet.ChipEffectSet	Man page
fromDataSet.FirmaSet	Man page
fromDataSet.GenomeInformation	Man page
fromDataSet.ResidualSet	Man page
fromDataSet.SnpInformation	Man page
fromDataSet.WeightsSet	Man page
fromFile,AffymetrixCdfFile-method	Man page
fromFile,AffymetrixCelFile-method	Man page
fromFile,AffymetrixPgfFile-method	Man page
fromFile,AromaChipTypeAnnotationFile-method	Man page
fromFile,CnagCfhFile-method	Man page
fromFile.AffymetrixCdfFile	Man page
fromFile.AffymetrixCelFile	Man page
fromFile.AffymetrixCnChpFile	Man page
fromFile.AffymetrixPgfFile	Man page
fromFile.AromaChipTypeAnnotationFile	Man page
fromFile.CnagCfhFile	Man page
fromFile.DChipCdfBinFile	Man page
fromFile.DChipDcpFile	Man page
getACSFile	Man page
getACSFile.AffymetrixCdfFile	Man page
getAM,ChipEffectFile-method	Man page
getAM,ChipEffectSet-method	Man page
getAM.ChipEffectFile	Man page
getAM.ChipEffectSet	Man page
getAlias,GenericReporter-method	Man page
getAlias,Model-method	Man page
getAlias.ArrayExplorer	Man page
getAlias.GenericReporter	Man page
getAlias.Model	Man page
getAlias.TransformReport	Man page
getAlleleCellPairs	Man page
getAlleleCellPairs,AffymetrixCdfFile-method	Man page
getAlleleCellPairs.AffymetrixCdfFile	Man page
getAlleleProbePairs	Man page
getAlleleProbePairs,AffymetrixCdfFile-method	Man page
getAlleleProbePairs.AffymetrixCdfFile	Man page
getAlleleProbePairs2	Man page
getAlleleProbePairs2.AffymetrixCdfFile	Man page
getAlleleProbePairs3	Man page
getAlleleProbePairs3,AffymetrixCdfFile-method	Man page
getAlleleProbePairs3.AffymetrixCdfFile	Man page
getAm	Man page
getAm.AffymetrixCelFile	Man page
getAromaCellMatchScoreFile	Man page
getAromaCellMatchScoreFile.MatNormalization	Man page
getAromaCellPositionFile	Man page
getAromaCellPositionFile.MatSmoothing	Man page
getAromaCellSequenceFile	Man page
getAromaCellSequenceFile.AbstractProbeSequenceNormalization	Man page
getAromaCellSequenceFile.AffymetrixCdfFile	Man page
getAromaUfcFile	Man page
getAromaUfcFile.FragmentEquivalentClassNormalization	Man page
getAromaUflFile.UflSnpInformation	Man page
getAromaUgpFile.UgpGenomeInformation	Man page
getAromaUnitFracBCnBinarySet	Man page
getAromaUnitFracBCnBinarySet.default	Man page
getAromaUnitTotalCnBinarySet	Man page
getAromaUnitTotalCnBinarySet.default	Man page
getArrayNames	Man page
getArrayNames.AffymetrixAptSummaryFile	Man page
getArraysOfInput.ArrayExplorer	Man page
getAsFullCelFile	Man page
getAsFullCelFile.ChipEffectFile	Man page
getAsFullCelSet	Man page
getAsFullCelSet.ChipEffectSet	Man page
getAsteriskTags.AdditiveCovariatesNormalization	Man page
getAsteriskTags.AffineCnPlm	Man page
getAsteriskTags.AffinePlm	Man page
getAsteriskTags.AffineSnpPlm	Man page
getAsteriskTags.AlleleSummation	Man page
getAsteriskTags.AllelicCrosstalkCalibration	Man page
getAsteriskTags.ArrayExplorer	Man page
getAsteriskTags.AvgCnPlm	Man page
getAsteriskTags.AvgPlm	Man page
getAsteriskTags.AvgSnpPlm	Man page
getAsteriskTags.BaseCountNormalization	Man page
getAsteriskTags.BasePositionNormalization	Man page
getAsteriskTags.CrlmmModel	Man page
getAsteriskTags.ExonRmaPlm	Man page
getAsteriskTags.FirmaModel	Man page
getAsteriskTags.FragmentEquivalentClassNormalization	Man page
getAsteriskTags.FragmentLengthNormalization	Man page
getAsteriskTags.GenericReporter	Man page
getAsteriskTags.HetLogAddCnPlm	Man page
getAsteriskTags.HetLogAddPlm	Man page
getAsteriskTags.HetLogAddSnpPlm	Man page
getAsteriskTags.LimmaBackgroundCorrection	Man page
getAsteriskTags.MatNormalization	Man page
getAsteriskTags.MbeiCnPlm	Man page
getAsteriskTags.MbeiPlm	Man page
getAsteriskTags.MbeiSnpPlm	Man page
getAsteriskTags.Model	Man page
getAsteriskTags.NormExpBackgroundCorrection	Man page
getAsteriskTags.ProbeLevelModel	Man page
getAsteriskTags.ProbeLevelTransform3	Man page
getAsteriskTags.QualityAssessmentModel	Man page
getAsteriskTags.ReseqCrosstalkCalibration	Man page
getAsteriskTags.RmaCnPlm	Man page
getAsteriskTags.RmaPlm	Man page
getAsteriskTags.RmaSnpPlm	Man page
getAsteriskTags.ScaleNormalization	Man page
getAsteriskTags.SmoothMultiarrayModel	Man page
getAsteriskTags.SmoothRmaModel	Man page
getAsteriskTags.SmoothSaModel	Man page
getAsteriskTags.SnpChipEffectGroupMerge	Man page
getAsteriskTags.UnitModel	Man page
getAverage	Man page
getAverage.AffymetrixCelSet	Man page
getAverage.CnagCfhSet	Man page
getAverageAsinh	Man page
getAverageAsinh.AffymetrixCelSet	Man page
getAverageAsinh.CnagCfhSet	Man page
getAverageFile,AffymetrixCelSet-method	Man page
getAverageFile,CnagCfhSet-method	Man page
getAverageFile.AffymetrixCelSet	Man page
getAverageFile.ChipEffectSet	Man page
getAverageFile.CnChipEffectSet	Man page
getAverageFile.CnagCfhSet	Man page
getAverageFile.ExonChipEffectSet	Man page
getAverageFile.ResidualSet	Man page
getAverageFile.SnpChipEffectSet	Man page
getAverageFile.WeightsSet	Man page
getAverageLog	Man page
getAverageLog.AffymetrixCelSet	Man page
getAverageLog.CnagCfhSet	Man page
getBandwidth	Man page
getBandwidth.SmoothMultiarrayModel	Man page
getBaseline	Man page
getBaseline,ChipEffectSet-method	Man page
getBaseline.ChipEffectSet	Man page
getBaseline.CnChipEffectSet	Man page
getBaseline.SnpChipEffectSet	Man page
getBlockSizes	Man page
getBlockSizes.SpatialRowColumnNormalization	Man page
getCalculateResidualsFunction	Man page
getCalculateResidualsFunction.AvgPlm	Man page
getCalculateResidualsFunction.ProbeLevelModel	Man page
getCalculateResidualsFunction.RmaPlm	Man page
getCallSet	Man page
getCallSet.CrlmmModel	Man page
getCalls.DChipDcpFile	Man page
getCdf	Man page
getCdf,AffymetrixCelFile-method	Man page
getCdf,AffymetrixCelSet-method	Man page
getCdf,CnagCfhFile-method	Man page
getCdf,CnagCfhSet-method	Man page
getCdf,Model-method	Man page
getCdf.AdditiveCovariatesNormalization	Man page
getCdf.AffymetrixCelFile	Man page
getCdf.AffymetrixCelSet	Man page
getCdf.AffymetrixCnChpFile	Man page
getCdf.AffymetrixCnChpSet	Man page
getCdf.AffymetrixProbeTabFile	Man page
getCdf.AffymetrixTsvFile	Man page
getCdf.AromaUnitTabularBinaryFile	Man page
getCdf.ChipEffectGroupMerge	Man page
getCdf.CnagCfhFile	Man page
getCdf.CnagCfhSet	Man page
getCdf.FirmaModel	Man page
getCdf.FragmentEquivalentClassNormalization	Man page
getCdf.FragmentLengthNormalization	Man page
getCdf.GcContentNormalization	Man page
getCdf.Model	Man page
getCdf.QualityAssessmentModel	Man page
getCdf.TransformReport	Man page
getCdfBin	Man page
getCdfBin.DChipDcpSet	Man page
getCellDim	Man page
getCellDim.DChipCdfBinFile	Man page
getCellIndices	Man page
getCellIndices,AffymetrixCdfFile-method	Man page
getCellIndices,ChipEffectFile-method	Man page
getCellIndices,CnChipEffectFile-method	Man page
getCellIndices,CnProbeAffinityFile-method	Man page
getCellIndices,ExonChipEffectFile-method	Man page
getCellIndices,ExonProbeAffinityFile-method	Man page
getCellIndices,FirmaFile-method	Man page
getCellIndices,ProbeAffinityFile-method	Man page
getCellIndices,ResidualFile-method	Man page
getCellIndices,SnpChipEffectFile-method	Man page
getCellIndices,SnpProbeAffinityFile-method	Man page
getCellIndices,UnitModel-method	Man page
getCellIndices,WeightsFile-method	Man page
getCellIndices.AffymetrixCdfFile	Man page
getCellIndices.ChipEffectFile	Man page
getCellIndices.ChipEffectSet	Man page
getCellIndices.CnChipEffectFile	Man page
getCellIndices.CnPlm	Man page
getCellIndices.CnProbeAffinityFile	Man page
getCellIndices.ExonChipEffectFile	Man page
getCellIndices.ExonProbeAffinityFile	Man page
getCellIndices.ExonRmaPlm	Man page
getCellIndices.FirmaFile	Man page
getCellIndices.FirmaSet	Man page
getCellIndices.ProbeAffinityFile	Man page
getCellIndices.ResidualFile	Man page
getCellIndices.ResidualSet	Man page
getCellIndices.SnpChipEffectFile	Man page
getCellIndices.SnpPlm	Man page
getCellIndices.SnpProbeAffinityFile	Man page
getCellIndices.UnitModel	Man page
getCellIndices.WeightsFile	Man page
getCellIndices.WeightsSet	Man page
getCellMap,ChipEffectFile-method	Man page
getCellMap.ChipEffectFile	Man page
getCellMapForMainCdf	Man page
getCellMapForMainCdf.ChipEffectFile	Man page
getCellQuartets	Man page
getCellQuartets.AffymetrixCdfFile	Man page
getCellsTo	Man page
getCellsTo.ProbeLevelTransform3	Man page
getCellsToFit	Man page
getCellsToFit.ProbeLevelTransform3	Man page
getCellsToInternal	Man page
getCellsToInternal.ProbeLevelTransform3	Man page
getCellsToUpdate	Man page
getCellsToUpdate.ProbeLevelTransform3	Man page
getChipEffectFileClass	Man page
getChipEffectFileClass.ChipEffectSet	Man page
getChipEffectFileClass.CnChipEffectSet	Man page
getChipEffectFileClass.ExonChipEffectSet	Man page
getChipEffectFileClass.SnpChipEffectSet	Man page
getChipEffectSet	Man page
getChipEffectSet,AlleleSummation-method	Man page
getChipEffectSet,ProbeLevelModel-method	Man page
getChipEffectSet.AlleleSummation	Man page
getChipEffectSet.CnPlm	Man page
getChipEffectSet.ExonRmaPlm	Man page
getChipEffectSet.ProbeLevelModel	Man page
getChipEffectSet.QualityAssessmentModel	Man page
getChipEffectSet.SnpPlm	Man page
getChipEffectSetClass	Man page
getChipEffectSetClass.AlleleSummation	Man page
getChipEffectSetClass.CnPlm	Man page
getChipEffectSetClass.ExonRmaPlm	Man page
getChipEffectSetClass.ProbeLevelModel	Man page
getChipEffectSetClass.SnpPlm	Man page
getChipEffects,ProbeLevelModel-method	Man page
getChipEffects.ProbeLevelModel	Man page
getChipType,AffymetrixCelFile-method	Man page
getChipType,AffymetrixCelSet-method	Man page
getChipType,CnagCfhFile-method	Man page
getChipType,GenomeInformation-method	Man page
getChipType,SnpInformation-method	Man page
getChipType.AffymetrixAptSummaryFile	Man page
getChipType.AffymetrixCdfFile	Man page
getChipType.AffymetrixCelFile	Man page
getChipType.AffymetrixCelSet	Man page
getChipType.AffymetrixCelSetReporter	Man page
getChipType.AffymetrixCnChpFile	Man page
getChipType.AffymetrixPgfFile	Man page
getChipType.AffymetrixProbeTabFile	Man page
getChipType.AffymetrixTsvFile	Man page
getChipType.AromaChipTypeAnnotationFile	Man page
getChipType.CnagCfhFile	Man page
getChipType.CrlmmModel	Man page
getChipType.DChipCdfBinFile	Man page
getChipType.DChipDcpSet	Man page
getChipType.GenomeInformation	Man page
getChipType.SnpInformation	Man page
getChipType.UflSnpInformation	Man page
getChipType.UgpGenomeInformation	Man page
getChromosomeStats	Man page
getChromosomeStats.GenomeInformation	Man page
getChromosomes.GenomeInformation	Man page
getChromosomes.UgpGenomeInformation	Man page
getCnNames	Man page
getCnNames,AffymetrixCdfFile-method	Man page
getCnNames.AffymetrixCdfFile	Man page
getColorMaps	Man page
getColorMaps.ArrayExplorer	Man page
getColorMaps.SpatialReporter	Man page
getColumnNames.AffymetrixProbeTabFile	Man page
getCombineAlleles	Man page
getCombineAlleles.CnChipEffectSet	Man page
getCombineAlleles.CnPlm	Man page
getConfidenceScoreSet	Man page
getConfidenceScoreSet.CrlmmModel	Man page
getCovariates	Man page
getCovariates.AdditiveCovariatesNormalization	Man page
getCovariates.GcContentNormalization2	Man page
getCrlmmParametersSet	Man page
getCrlmmParametersSet.CrlmmModel	Man page
getCrlmmPriors	Man page
getCrlmmPriors.CrlmmModel	Man page
getCrlmmSNPs	Man page
getCrlmmSNPs.CrlmmModel	Man page
getCrlmmSNPsOnChrX	Man page
getCrlmmSNPsOnChrX.CrlmmModel	Man page
getCrlmmSplineParameters	Man page
getCrlmmSplineParameters.CrlmmModel	Man page
getData	Man page
getData,AffymetrixCelFile-method	Man page
getData,GenomeInformation-method	Man page
getData,SnpInformation-method	Man page
getData.AffymetrixCelFile	Man page
getData.AffymetrixCelSet	Man page
getData.AffymetrixCnChpFile	Man page
getData.AffymetrixProbeTabFile	Man page
getData.AffymetrixTsvFile	Man page
getData.CnagCfhSet	Man page
getData.GenomeInformation	Man page
getData.SnpInformation	Man page
getData.UflSnpInformation	Man page
getData.UgpGenomeInformation	Man page
getDataColumns	Man page
getDataColumns.GenomeInformation	Man page
getDataColumns.UflSnpInformation	Man page
getDataColumns.UgpGenomeInformation	Man page
getDataFlat	Man page
getDataFlat.ChipEffectFile	Man page
getDataFlat.FirmaFile	Man page
getDataFlat.ResidualFile	Man page
getDataFlat.WeightsFile	Man page
getDataPairs	Man page
getDataPairs.AllelicCrosstalkCalibration	Man page
getDataSet	Man page
getDataSet,AffymetrixCelSetReporter-method	Man page
getDataSet,ArrayExplorer-method	Man page
getDataSet,Model-method	Man page
getDataSet.AffymetrixCelSetReporter	Man page
getDataSet.ArrayExplorer	Man page
getDataSet.FirmaModel	Man page
getDataSet.Model	Man page
getDataSet.QualityAssessmentModel	Man page
getDefaultColumnNames.AromaCellMatchScoreFile	Man page
getDefaultColumnNames.AromaUfcFile	Man page
getDefaultExtension.AffymetrixCdfFile	Man page
getDefaultExtension.AffymetrixCsvFile	Man page
getDefaultExtension.AffymetrixCsvGenomeInformation	Man page
getDefaultExtension.AffymetrixNetAffxCsvFile	Man page
getDefaultExtension.AffymetrixPgfFile	Man page
getDefaultExtension.AffymetrixTsvFile	Man page
getDefaultExtension.AromaCellMatchScoreFile	Man page
getDefaultExtension.AromaChipTypeAnnotationFile	Man page
getDefaultFullName.AffymetrixFileSet	Man page
getDefaultFullName.CnagCfhSet	Man page
getDefaultSettings	Man page
getDefaultSettings.AromaAffymetrix	Man page
getDefaultSettings.Package	Man page
getDesignMatrix	Man page
getDesignMatrix.BaseCountNormalization	Man page
getDesignMatrix.BasePositionNormalization	Man page
getDesignMatrix.LinearModelProbeSequenceNormalization	Man page
getDesignMatrix.MatNormalization	Man page
getDimension	Man page
getDimension.AffymetrixCdfFile	Man page
getDimension.AffymetrixPgfFile	Man page
getExclCells	Man page
getExclCells.DChipQuantileNormalization	Man page
getExclCells.QuantileNormalization	Man page
getExcludes	Man page
getExcludes.DChipDcpFile	Man page
getExclusiveUnitSubsets	Man page
getExclusiveUnitSubsets.FragmentEquivalentClassNormalization	Man page
getExpandedCellMap	Man page
getExpandedCellMap.ChipEffectFile	Man page
getExpandedCellMap.CnChipEffectFile	Man page
getExpandedCellMap.SnpChipEffectFile	Man page
getExpectedOutputFullnames.MatSmoothing	Man page
getExtensionPattern.AffymetrixCdfFile	Man page
getExtensionPattern.AffymetrixCelFile	Man page
getExtensionPattern.AffymetrixCnChpFile	Man page
getExtensionPattern.AffymetrixCsvFile	Man page
getExtensionPattern.AffymetrixPgfFile	Man page
getExtensionPattern.AffymetrixTsvFile	Man page
getExtensionPattern.AromaCellMatchScoreFile	Man page
getExtensionPattern.AromaUfcFile	Man page
getExtensionPattern.CnagCfhFile	Man page
getExtensionPattern.DChipDcpFile	Man page
getField	Man page
getField.AffymetrixTsvFile	Man page
getFields.SnpInformation	Man page
getFields.UflSnpInformation	Man page
getFileClass.FirmaSet	Man page
getFileFormat	Man page
getFileFormat.AffymetrixCdfFile	Man page
getFileFormat.AffymetrixCelFile	Man page
getFileFormat.AffymetrixCnChpFile	Man page
getFileFormat.DChipCdfBinFile	Man page
getFileFormat.DChipDcpFile	Man page
getFileSet	Man page
getFileSet.AffymetrixFileSetReporter	Man page
getFileSetClass	Man page
getFileSetClass.FirmaModel	Man page
getFilenameExtension.AromaCellMatchScoreFile	Man page
getFilenameExtension.AromaUfcFile	Man page
getFilteredFragmentLengths	Man page
getFilteredFragmentLengths.FragmentLengthNormalization	Man page
getFirmaScores	Man page
getFirmaScores,FirmaModel-method	Man page
getFirmaScores.FirmaModel	Man page
getFirmaSet	Man page
getFirmaSet,FirmaModel-method	Man page
getFirmaSet.FirmaModel	Man page
getFirstCellIndices	Man page
getFirstCellIndices.AffymetrixCdfFile	Man page
getFirstCellPerUnitIndices	Man page
getFirstCellPerUnitIndices.ExonChipEffectSet	Man page
getFit	Man page
getFit.BasePositionNormalization	Man page
getFitSingleCellUnitFunction	Man page
getFitSingleCellUnitFunction.UnitModel	Man page
getFitUnitFunction	Man page
getFitUnitFunction.CnPlm	Man page
getFitUnitFunction.FirmaModel	Man page
getFitUnitFunction.MultiArrayUnitModel	Man page
getFitUnitFunction.SingleArrayUnitModel	Man page
getFitUnitFunction.UnitModel	Man page
getFitUnitGroupFunction	Man page
getFitUnitGroupFunction,AffinePlm-method	Man page
getFitUnitGroupFunction,AvgPlm-method	Man page
getFitUnitGroupFunction,ExonRmaPlm-method	Man page
getFitUnitGroupFunction,FirmaModel-method	Man page
getFitUnitGroupFunction,HetLogAddPlm-method	Man page
getFitUnitGroupFunction,MbeiPlm-method	Man page
getFitUnitGroupFunction,MultiArrayUnitModel-method	Man page
getFitUnitGroupFunction,RmaPlm-method	Man page
getFitUnitGroupFunction,SingleArrayUnitModel-method	Man page
getFitUnitGroupFunction.AffinePlm	Man page
getFitUnitGroupFunction.AvgPlm	Man page
getFitUnitGroupFunction.ExonRmaPlm	Man page
getFitUnitGroupFunction.FirmaModel	Man page
getFitUnitGroupFunction.HetLogAddPlm	Man page
getFitUnitGroupFunction.MbeiPlm	Man page
getFitUnitGroupFunction.MultiArrayUnitModel	Man page
getFitUnitGroupFunction.RmaPlm	Man page
getFitUnitGroupFunction.SingleArrayUnitModel	Man page
getFitUnitGroupFunction.SmoothMultiarrayModel	Man page
getFitUnitGroupFunction.SmoothRmaModel	Man page
getFitUnitGroupFunction.SmoothSaModel	Man page
getFragmentLengths	Man page
getFragmentLengths.AffymetrixTsvFile	Man page
getFragmentLengths.SnpInformation	Man page
getFragmentLengths.UflSnpInformation	Man page
getFragmentStarts	Man page
getFragmentStarts.SnpInformation	Man page
getFragmentStarts.UflSnpInformation	Man page
getFragmentStops	Man page
getFragmentStops.SnpInformation	Man page
getFragmentStops.UflSnpInformation	Man page
getFullName,Model-method	Man page
getFullName,TransformReport-method	Man page
getFullName.GenericReporter	Man page
getFullName.Model	Man page
getFullName.QualityAssessmentModel	Man page
getFullName.TransformReport	Man page
getFullNames.ChipEffectSetTuple	Man page
getGc	Man page
getGc.AffymetrixTsvFile	Man page
getGcContent	Man page
getGcContent.GcContentNormalization	Man page
getGenomeBuild	Man page
getGenomeBuild.AffymetrixNetAffxCsvFile	Man page
getGenomeInformation	Man page
getGenomeInformation,AffymetrixCdfFile-method	Man page
getGenomeInformation.AffymetrixCdfFile	Man page
getGroupDirections	Man page
getGroupDirections.AffymetrixCdfFile	Man page
getHeader,AffymetrixCdfFile-method	Man page
getHeader,AffymetrixCelFile-method	Man page
getHeader,AffymetrixPgfFile-method	Man page
getHeader,AromaChipTypeAnnotationFile-method	Man page
getHeader,CnagCfhFile-method	Man page
getHeader.AffymetrixCdfFile	Man page
getHeader.AffymetrixCelFile	Man page
getHeader.AffymetrixCnChpFile	Man page
getHeader.AffymetrixPgfFile	Man page
getHeader.AromaChipTypeAnnotationFile	Man page
getHeader.CnagCfhFile	Man page
getHeader.DChipCdfBinFile	Man page
getHeader.DChipDcpFile	Man page
getHeaderAttributes	Man page
getHeaderAttributes.AffymetrixNetAffxCsvFile	Man page
getHeaderLength	Man page
getHeaderLength.CnagCfhFile	Man page
getHeaderV3	Man page
getHeaderV3.AffymetrixCelFile	Man page
getIdentifier	Man page
getIdentifier.AffymetrixCelFile	Man page
getIdentifier.AffymetrixCelSet	Man page
getIdentifier.AffymetrixFileSet	Man page
getIdentifier.CnagCfhFile	Man page
getIdentifier.CnagCfhSet	Man page
getImage,AffymetrixCelFile-method	Man page
getImage.AffymetrixCdfFile	Man page
getImage.AffymetrixCelFile	Man page
getImage.AromaUnitTabularBinaryFile	Man page
getImage.ResidualFile	Man page
getImage.WeightsFile	Man page
getIndexToRowMap	Man page
getIndexToRowMap.AffymetrixProbeTabFile	Man page
getInputDataSet,TransformReport-method	Man page
getInputDataSet.TransformReport	Man page
getInputName	Man page
getInputName.AffymetrixFileSetReporter	Man page
getInputName.GenericReporter	Man page
getInputTags	Man page
getInputTags.AffymetrixFileSetReporter	Man page
getInputTags.GenericReporter	Man page
getIntensities	Man page
getIntensities,AffymetrixCelSet-method	Man page
getIntensities.AffymetrixCelSet	Man page
getLabel.Model	Man page
getListOfCdfs	Man page
getListOfCdfs.AffymetrixCelSetTuple	Man page
getListOfGenomeInformations	Man page
getListOfGenomeInformations.ChromosomalModel	Man page
getListOfPriors	Man page
getListOfPriors.MultiArrayUnitModel	Man page
getListOfReporters	Man page
getListOfReporters.ArrayExplorer	Man page
getListOfUnitNamesFiles.AffymetrixCelSetTuple	Man page
getListOfUnitNamesFiles.ArrayExplorer	Man page
getListOfUnitTypesFiles.AffymetrixCelSetTuple	Man page
getListOfUnitTypesFiles.ArrayExplorer	Man page
getMainCdf	Man page
getMainCdf.AffymetrixCdfFile	Man page
getMainPath.GenericReporter	Man page
getMergeFunction	Man page
getMergeFunction.ChipEffectGroupMerge	Man page
getMergeFunction.SnpChipEffectGroupMerge	Man page
getMergeGroups	Man page
getMergeGroups.ExonChipEffectSet	Man page
getMergeStrands	Man page
getMergeStrands.SnpChipEffectSet	Man page
getMergeStrands.SnpPlm	Man page
getMonocellCdf	Man page
getMonocellCdf.AffymetrixCdfFile	Man page
getName,GenericReporter-method	Man page
getName,Model-method	Man page
getName,TransformReport-method	Man page
getName.AffymetrixPlatform	Man page
getName.FirmaModel	Man page
getName.GenericReporter	Man page
getName.Model	Man page
getName.QualityAssessmentModel	Man page
getName.TransformReport	Man page
getNameOfInput.ArrayExplorer	Man page
getNetAffxBuild	Man page
getNetAffxBuild.AffymetrixNetAffxCsvFile	Man page
getNetAffxDate	Man page
getNetAffxDate.AffymetrixNetAffxCsvFile	Man page
getNormalEquations	Man page
getNormalEquations.LinearModelProbeSequenceNormalization	Man page
getNormalizeSignalsOne	Man page
getNormalizeSignalsOne.ScaleNormalization3	Man page
getNormalizeSignalsOne.UnitTypeScaleNormalization	Man page
getNormalizedIntensities	Man page
getNormalizedIntensities.DChipDcpFile	Man page
getNumberOfFilesAveraged.CnChipEffectFile	Man page
getOrderedFragmentPairMap	Man page
getOrderedFragmentPairMap.AromaUfcFile	Man page
getOrderedFragmentPairs	Man page
getOrderedFragmentPairs.AromaUfcFile	Man page
getOutputDataSet,Transform-method	Man page
getOutputDataSet,TransformReport-method	Man page
getOutputDataSet.Transform	Man page
getOutputDataSet.TransformReport	Man page
getOutputDataSet00	Man page
getOutputDataSet00.AdditiveCovariatesNormalization	Man page
getOutputDataSet00.FragmentEquivalentClassNormalization	Man page
getOutputDataSet00.FragmentLengthNormalization	Man page
getOutputDataSet00.GcContentNormalization	Man page
getOutputFiles.Transform	Man page
getOutputIdentifier	Man page
getOutputIdentifier.QuantileNormalization	Man page
getOutputTuple	Man page
getOutputTuple.SmoothMultiarrayModel	Man page
getParameter	Man page
getParameter.AffymetrixAptSummaryFile	Man page
getParameters.AbstractProbeSequenceNormalization	Man page
getParameters.AdditiveCovariatesNormalization	Man page
getParameters.AllelicCrosstalkCalibration	Man page
getParameters.AvgPlm	Man page
getParameters.BackgroundCorrection	Man page
getParameters.BaseCountNormalization	Man page
getParameters.BasePositionNormalization	Man page
getParameters.ChipEffectFile	Man page
getParameters.ChipEffectGroupMerge	Man page
getParameters.CnChipEffectFile	Man page
getParameters.CnPlm	Man page
getParameters.CrlmmModel	Man page
getParameters.DChipQuantileNormalization	Man page
getParameters.ExonChipEffectFile	Man page
getParameters.ExonRmaPlm	Man page
getParameters.FragmentEquivalentClassNormalization	Man page
getParameters.FragmentLengthNormalization	Man page
getParameters.GcContentNormalization	Man page
getParameters.GcRmaBackgroundCorrection	Man page
getParameters.LimmaBackgroundCorrection	Man page
getParameters.MatNormalization	Man page
getParameters.MatSmoothing	Man page
getParameters.NormExpBackgroundCorrection	Man page
getParameters.OpticalBackgroundCorrection	Man page
getParameters.ProbeAffinityFile	Man page
getParameters.ProbeLevelTransform3	Man page
getParameters.QuantileNormalization	Man page
getParameters.ReseqCrosstalkCalibration	Man page
getParameters.ResidualFile	Man page
getParameters.ResidualSet	Man page
getParameters.RmaBackgroundCorrection	Man page
getParameters.RmaPlm	Man page
getParameters.ScaleNormalization	Man page
getParameters.ScaleNormalization3	Man page
getParameters.SnpChipEffectFile	Man page
getParameters.SnpChipEffectGroupMerge	Man page
getParameters.SnpPlm	Man page
getParameters.SpatialRowColumnNormalization	Man page
getParameters.UnitModel	Man page
getParameters.UnitTypeScaleNormalization	Man page
getParameters.WeightsFile	Man page
getParameters.WeightsSet	Man page
getPath,Model-method	Man page
getPath,TransformReport-method	Man page
getPath.AffymetrixCelSetReporter	Man page
getPath.GenericReporter	Man page
getPath.Model	Man page
getPath.QualityAssessmentModel	Man page
getPath.TransformReport	Man page
getPcuTheta	Man page
getPcuTheta.ChromosomalModel	Man page
getPlasqTypes	Man page Source code
getPlatform.AffymetrixCdfFile	Man page
getPlatform.AffymetrixCelFile	Man page
getPlatform.AffymetrixCelSet	Man page
getPlatform.AffymetrixPgfFile	Man page
getPlatform.AromaChipTypeAnnotationFile	Man page
getPlatform.DChipCdfBinFile	Man page
getPlatformDesignDB	Man page
getPlatformDesignDB.CrlmmModel	Man page
getPlm	Man page
getPlm.FirmaModel	Man page
getPlm.QualityAssessmentModel	Man page
getPosition.AffymetrixTsvFile	Man page
getPositionChipTypeUnit	Man page
getPositionChipTypeUnit.ChromosomalModel	Man page
getPositionChipTypeUnit.CopyNumberSegmentationModel	Man page
getPositions,GenomeInformation-method	Man page
getPositions.GenomeInformation	Man page
getProbeAffinities,ProbeLevelModel-method	Man page
getProbeAffinities.ProbeLevelModel	Man page
getProbeAffinityFile	Man page
getProbeAffinityFile,ProbeLevelModel-method	Man page
getProbeAffinityFile.AffinePlm	Man page
getProbeAffinityFile.AvgPlm	Man page
getProbeAffinityFile.CnPlm	Man page
getProbeAffinityFile.ExonRmaPlm	Man page
getProbeAffinityFile.MbeiPlm	Man page
getProbeAffinityFile.ProbeLevelModel	Man page
getProbeAffinityFile.RmaPlm	Man page
getProbeAffinityFile.SnpPlm	Man page
getProbeSequenceData	Man page
getProbeSequenceData.AffymetrixCdfFile	Man page
getProbesetIds	Man page
getProbesetIds.AffymetrixAptSummaryFile	Man page
getQuantificationScale	Man page
getQuantificationScale.AffymetrixAptSummaryFile	Man page
getRawIntensities	Man page
getRawIntensities.DChipDcpFile	Man page
getReadArguments.AffymetrixAptSummaryFile	Man page
getRectangle	Man page
getRectangle.AffymetrixCelFile	Man page
getReference.SpatialReporter	Man page
getRegions.profileCGH	Man page
getReportSet	Man page
getReportSet.GenericReporter	Man page
getReportSet.SpatialReporter	Man page
getResidualFileClass	Man page
getResidualFileClass.ResidualSet	Man page
getResidualSet	Man page
getResidualSet.ProbeLevelModel	Man page
getResidualSetClass	Man page
getResidualSetClass.ProbeLevelModel	Man page
getResiduals	Man page
getResiduals,QualityAssessmentModel-method	Man page
getResiduals.QualityAssessmentModel	Man page
getRestructor	Man page
getRestructor.AffymetrixCdfFile	Man page
getRlmFitFunctions	Man page
getRlmFitFunctions.RmaPlm	Man page
getRootPath,Model-method	Man page
getRootPath.AlleleSummation	Man page
getRootPath.ChipEffectTransform	Man page
getRootPath.CrlmmModel	Man page
getRootPath.FirmaModel	Man page
getRootPath.GenericReporter	Man page
getRootPath.Model	Man page
getRootPath.ProbeLevelModel	Man page
getRootPath.ProbeLevelTransform	Man page
getRootPath.QualityAssessmentModel	Man page
getRootPath.SmoothMultiarrayModel	Man page
getRootPath.SmoothRmaModel	Man page
getRootPath.TransformReport	Man page
getSetTuple.ArrayExplorer	Man page
getSetsOfProbes	Man page
getSetsOfProbes.AllelicCrosstalkCalibration	Man page
getSetsOfProbes.ReseqCrosstalkCalibration	Man page
getSettings	Man page
getSettings.Package	Man page
getSignalTransform	Man page
getSignalTransform.BasePositionNormalization	Man page
getSignalTransform.LinearModelProbeSequenceNormalization	Man page
getSnpInformation	Man page
getSnpInformation.AffymetrixCdfFile	Man page
getSnpNames	Man page
getSnpNames,AffymetrixCdfFile-method	Man page
getSnpNames.AffymetrixCdfFile	Man page
getSpar	Man page
getSpar.SpatialRowColumnNormalization	Man page
getSteps	Man page
getSteps.ASCRMAv2	Man page
getSteps.AromaPipeline	Man page
getSubsetOfCellIndices	Man page
getSubsetOfCellIndices.AffymetrixCdfFile	Man page
getSubsetOfUnits	Man page
getSubsetOfUnits.AffymetrixCdfFile	Man page
getSubsetToAvg	Man page
getSubsetToAvg.AllelicCrosstalkCalibration	Man page
getSubsetToAvg.QuantileNormalization	Man page
getSubsetToAvg.ReseqCrosstalkCalibration	Man page
getSubsetToAvg.ScaleNormalization	Man page
getSubsetToFit	Man page
getSubsetToFit.AdditiveCovariatesNormalization	Man page
getSubsetToFit.FragmentEquivalentClassNormalization	Man page
getSubsetToFit.FragmentLengthNormalization	Man page
getSubsetToFit.GcContentNormalization	Man page
getSubsetToUpdate	Man page
getSubsetToUpdate.BackgroundCorrection	Man page
getSubsetToUpdate.DChipQuantileNormalization	Man page
getSubsetToUpdate.QuantileNormalization	Man page
getSubsetToUpdate.ScaleNormalization	Man page
getSubsetToUpdate0	Man page
getSubsetToUpdate0.LimmaBackgroundCorrection	Man page
getTags,GenericReporter-method	Man page
getTags,Model-method	Man page
getTags,TransformReport-method	Man page
getTags.FirmaModel	Man page
getTags.GenericReporter	Man page
getTags.Model	Man page
getTags.QualityAssessmentModel	Man page
getTags.TransformReport	Man page
getTagsOfInput.ArrayExplorer	Man page
getTargetAverages	Man page
getTargetAverages.FragmentEquivalentClassNormalization	Man page
getTargetDistribution	Man page
getTargetDistribution.QuantileNormalization	Man page
getTargetDistributionIdentifier	Man page
getTargetDistributionIdentifier.QuantileNormalization	Man page
getTargetDistributionPathname	Man page
getTargetDistributionPathname.QuantileNormalization	Man page
getTargetFile	Man page
getTargetFile.AbstractProbeSequenceNormalization	Man page
getTargetFunction	Man page
getTargetFunction.GcContentNormalization	Man page
getTargetFunctions	Man page
getTargetFunctions.AdditiveCovariatesNormalization	Man page
getTargetFunctions.FragmentLengthNormalization	Man page
getThetaStds	Man page
getThetaStds.DChipDcpFile	Man page
getThetas	Man page
getThetas.DChipDcpFile	Man page
getThetasAB	Man page
getThetasAB.DChipDcpFile	Man page
getTimeStamp	Man page
getTimeStamp.AffymetrixAptSummaryFile	Man page
getTimestamp	Man page
getTimestamp,AffymetrixCelFile-method	Man page
getTimestamp.AffymetrixCelFile	Man page
getTimestamp.AffymetrixCnChpFile	Man page
getTimestamp.CnagCfhFile	Man page
getTimestamps	Man page
getTimestamps.AffymetrixCelSet	Man page
getTimestamps.CnagCfhSet	Man page
getUniqueCdf	Man page
getUniqueCdf.AffymetrixCdfFile	Man page
getUnitGroupCellArrayMap	Man page
getUnitGroupCellArrayMap.ChipEffectFile	Man page
getUnitGroupCellChromosomePositionMap	Man page
getUnitGroupCellChromosomePositionMap.AffymetrixCdfFile	Man page
getUnitGroupCellChromosomePositionMap.ChipEffectFile	Man page
getUnitGroupCellMap	Man page
getUnitGroupCellMap,ChipEffectFile-method	Man page
getUnitGroupCellMap.AffymetrixCdfFile	Man page
getUnitGroupCellMap.AffymetrixCelSet	Man page
getUnitGroupCellMap.ChipEffectFile	Man page
getUnitGroupCellMap.FirmaFile	Man page
getUnitGroupCellMap.ResidualFile	Man page
getUnitGroupCellMap.WeightsFile	Man page
getUnitGroupCellMapWithMonocell	Man page
getUnitGroupCellMapWithMonocell.AffymetrixCdfFile	Man page
getUnitGroupCellMapWithUnique	Man page
getUnitGroupCellMapWithUnique.AffymetrixCdfFile	Man page
getUnitGroupCellMatrixMap	Man page
getUnitGroupCellMatrixMap.ChipEffectFile	Man page
getUnitGroupNamesFromUgcMap	Man page
getUnitGroupNamesFromUgcMap.AffymetrixCdfFile	Man page
getUnitIndices	Man page
getUnitIndices,GenomeInformation-method	Man page
getUnitIndices.GenomeInformation	Man page
getUnitIntensities	Man page
getUnitIntensities,AffymetrixCelSet-method	Man page
getUnitIntensities.AffymetrixCelSet	Man page
getUnitNames,AffymetrixCdfFile-method	Man page
getUnitNames,AffymetrixPgfFile-method	Man page
getUnitNames.AffymetrixCdfFile	Man page
getUnitNames.AffymetrixNetAffxCsvFile	Man page
getUnitNames.AffymetrixPgfFile	Man page
getUnitNames.DChipCdfBinFile	Man page
getUnitNamesFile.AffymetrixCdfFile	Man page
getUnitNamesFile.AffymetrixCelFile	Man page
getUnitNamesFile.AffymetrixCelSet	Man page
getUnitNamesFile.AffymetrixCnChpFile	Man page
getUnitNamesFile.AffymetrixPgfFile	Man page
getUnitNamesFile.AffymetrixPlatform	Man page
getUnitNamesFile.TransformReport	Man page
getUnitReadMap	Man page
getUnitReadMap.AffymetrixCnChpFile	Man page
getUnitSizes	Man page
getUnitSizes.DChipCdfBinFile	Man page
getUnitTypes,AffymetrixCdfFile-method	Man page
getUnitTypes.AffymetrixCdfFile	Man page
getUnitTypesFile.AffymetrixCdfFile	Man page
getUnitTypesFile.AffymetrixCelFile	Man page
getUnitTypesFile.AffymetrixCelSet	Man page
getUnitTypesFile.AffymetrixCnChpFile	Man page
getUnitTypesFile.AffymetrixPlatform	Man page
getUnitTypesFile.TransformReport	Man page
getUnitsOnChromosome.GenomeInformation	Man page
getUnitsOnChromosome.UgpGenomeInformation	Man page
getUnitsOnChromosomes.GenomeInformation	Man page
getUnitsTo	Man page
getUnitsTo.ProbeLevelTransform3	Man page
getUnitsToFit	Man page
getUnitsToFit.CrlmmModel	Man page
getUnitsToFit.ProbeLevelTransform3	Man page
getUnitsToUpdate	Man page
getUnitsToUpdate.ProbeLevelTransform3	Man page
getWeights,QualityAssessmentModel-method	Man page
getWeights.QualityAssessmentModel	Man page
getWeightsFileClass	Man page
getWeightsFileClass.WeightsSet	Man page
getWeightsSet	Man page
getWeightsSet.ProbeLevelModel	Man page
getWeightsSetClass	Man page
getWeightsSetClass.ProbeLevelModel	Man page
getXAM,ChipEffectFile-method	Man page
getXAM,ChipEffectSet-method	Man page
getXAM.ChipEffectFile	Man page
getXAM.ChipEffectSet	Man page
getYY	Man page
getYY.TransformReport	Man page
groupUnitsByDimension	Man page
groupUnitsByDimension,AffymetrixCdfFile-method	Man page
groupUnitsByDimension.AffymetrixCdfFile	Man page
hasAlleleBFractions.CnChipEffectFile	Man page
hasAlleleBFractions.CnChipEffectSet	Man page
hasAlleleBFractions.CnChipEffectSetTuple	Man page
hasColumnHeader.AffymetrixProbeTabFile	Man page
hasMbeiData	Man page
hasMbeiData.DChipDcpFile	Man page
hasNormalizedData	Man page
hasNormalizedData.DChipDcpFile	Man page
hasStrandiness.CnChipEffectFile	Man page
hasStrandiness.CnChipEffectSet	Man page
hasStrandiness.CnChipEffectSetTuple	Man page
hasUnitReadMap	Man page
hasUnitReadMap.AffymetrixCnChpFile	Man page
hasUnitTypes	Man page
hasUnitTypes.AffymetrixCdfFile	Man page
highlight	Man page
highlight.AffymetrixCelFile	Man page
identifyCells	Man page
identifyCells.AffymetrixCdfFile	Man page
image270	Man page
image270,AffymetrixCelFile-method	Man page
image270.AffymetrixCelFile	Man page
importFrom.AromaUnitTabularBinaryFile	Man page
importFromAffymetrixNetAffxCsvFile	Man page
importFromAffymetrixNetAffxCsvFile.AromaUflFile	Man page
importFromAffymetrixNetAffxCsvFile.AromaUgpFile	Man page
importFromAffymetrixNetAffxCsvFile.AromaUnitGcContentFile	Man page
importFromAffymetrixNetAffxCsvFile.AromaUnitTabularBinaryFile	Man page
importFromAffymetrixProbeTabFile	Man page
importFromAffymetrixProbeTabFile.AromaCellSequenceFile	Man page
importFromAffymetrixTabularFile	Man page
importFromAffymetrixTabularFile.AromaUfcFile	Man page
importFromAffymetrixTabularFile.AromaUgpFile	Man page
importFromAffymetrixTabularFile.AromaUnitTabularBinaryFile	Man page
importFromApt	Man page
importFromApt,CnChipEffectSet-method	Man page
importFromApt.CnChipEffectSet	Man page
importFromBpMap	Man page
importFromBpMap.AromaCellMatchScoreFile	Man page
importFromBpMap.AromaCellSequenceFile	Man page
importFromDChip	Man page
importFromDChip,AffymetrixCelSet-method	Man page
importFromDChip,CnChipEffectSet-method	Man page
importFromDChip.AffymetrixCelSet	Man page
importFromDChip.CnChipEffectSet	Man page
importFromDChipGenomeInformation	Man page
importFromDChipGenomeInformation.AromaUnitTabularBinaryFile	Man page
importFromGenericTabularFile.AromaUnitTabularBinaryFile	Man page
importFromGenomeInformation	Man page
importFromGenomeInformation.AromaUgpFile	Man page
importFromGenomeInformation.AromaUnitTabularBinaryFile	Man page
indexOfMissingSequences	Man page
indexOfMissingSequences.AbstractProbeSequenceNormalization	Man page
inferMmFromPm	Man page
inferMmFromPm.AromaCellSequenceFile	Man page
inferParameters	Man page
inferParameters.CnChipEffectSet	Man page
inferParameters.SnpChipEffectSet	Man page
isCompatibleWithCdf	Man page
isCompatibleWithCdf.GenomeInformation	Man page
isCompatibleWithCdf.SnpInformation	Man page
isCompatibleWithCdf.UflSnpInformation	Man page
isCompatibleWithCdf.UgpGenomeInformation	Man page
isDuplicated	Man page
isDuplicated,AffymetrixCelSet-method	Man page
isDuplicated,CnagCfhSet-method	Man page
isDuplicated.AffymetrixCelSet	Man page
isDuplicated.CnagCfhSet	Man page
isMissing.AromaCellMatchScoreFile	Man page
isMonocellCdf	Man page
isMonocellCdf.AffymetrixCdfFile	Man page
isPm	Man page
isPm,AffymetrixCdfFile-method	Man page
isPm.AffymetrixCdfFile	Man page
isResequenceChip	Man page
isResequenceChip,AffymetrixCdfFile-method	Man page
isResequenceChip.AffymetrixCdfFile	Man page
isSnpChip	Man page
isSnpChip,AffymetrixCdfFile-method	Man page
isSnpChip.AffymetrixCdfFile	Man page
isUniqueCdf	Man page
isUniqueCdf.AffymetrixCdfFile	Man page
isUnitGroupCellMap	Man page
isUnitGroupCellMap.data.frame	Man page
isUnitGroupCellMap.default	Man page
isUnitGroupCellMap.matrix	Man page
justRMA	Man page
justRMA.AffymetrixCelSet	Man page
justRMA.default	Man page
justSNPRMA	Man page
justSNPRMA.AffymetrixCelSet	Man page
justSNPRMA.character	Man page
mapToUnitNamesFile	Man page
mapToUnitNamesFile.DChipCdfBinFile	Man page
mergeGroups	Man page
mergeGroups.ChipEffectFile	Man page
mergeStrands	Man page
mergeStrands.CnChipEffectFile	Man page
mergeStrands.SnpChipEffectFile	Man page
migrateTool	Man page
migrateTool.CopyNumberSegmentationModel	Man page
nbrOfArrays.AffymetrixAptSummaryFile	Man page
nbrOfArrays.AffymetrixCelSet	Man page
nbrOfArrays.AffymetrixCelSetReporter	Man page
nbrOfArrays.AffymetrixCnChpSet	Man page
nbrOfArrays.CnagCfhSet	Man page
nbrOfArrays.DChipDcpSet	Man page
nbrOfArrays.QualityAssessmentModel	Man page
nbrOfArrays.TransformReport	Man page
nbrOfCells.AffymetrixCdfFile	Man page
nbrOfCells.AffymetrixCelFile	Man page
nbrOfCells.AffymetrixPgfFile	Man page
nbrOfCells.CnagCfhFile	Man page
nbrOfCells.DChipCdfBinFile	Man page
nbrOfCells.DChipDcpFile	Man page
nbrOfCellsPerUnit	Man page
nbrOfCellsPerUnit.AffymetrixCdfFile	Man page
nbrOfCellsPerUnitGroup	Man page
nbrOfCellsPerUnitGroup.AffymetrixCdfFile	Man page
nbrOfChipTypes.ArrayExplorer	Man page
nbrOfColumns.AffymetrixCdfFile	Man page
nbrOfColumns.AffymetrixPgfFile	Man page
nbrOfEnzymes.AromaUfcFile	Man page
nbrOfEnzymes.SnpInformation	Man page
nbrOfEnzymes.UflSnpInformation	Man page
nbrOfGroupsPerUnit	Man page
nbrOfGroupsPerUnit,AffymetrixCdfFile-method	Man page
nbrOfGroupsPerUnit.AffymetrixCdfFile	Man page
nbrOfQcUnits	Man page
nbrOfQcUnits.AffymetrixCdfFile	Man page
nbrOfRows.AffymetrixCdfFile	Man page
nbrOfRows.AffymetrixPgfFile	Man page
nbrOfSnps	Man page
nbrOfSnps,AffymetrixCdfFile-method	Man page
nbrOfSnps.AffymetrixCdfFile	Man page
nbrOfSnps.CnagCfhFile	Man page
nbrOfSteps	Man page
nbrOfSteps.AromaPipeline	Man page
nbrOfUnits.AffymetrixCdfFile	Man page
nbrOfUnits.AffymetrixPgfFile	Man page
nbrOfUnits.DChipCdfBinFile	Man page
nbrOfUnits.DChipDcpFile	Man page
nbrOfUnits.GenomeInformation	Man page
nbrOfUnits.SnpInformation	Man page
nbrOfUnits.UflSnpInformation	Man page
nbrOfUnits.UgpGenomeInformation	Man page
normalizeOneArrayVector	Man page
normalizeOneArrayVector.FragmentEquivalentClassNormalization	Man page
normalizeQuantile	Man page
normalizeQuantile,AffymetrixCelFile-method	Man page
normalizeQuantile,AffymetrixCelSet-method	Man page
normalizeQuantile.AffymetrixCelFile	Man page
normalizeQuantile.AffymetrixCelSet	Man page
pdInfo2Cdf	Man page Source code
plasqGaussian	Man page Source code
plotAllelePairs	Man page
plotAllelePairs.AllelicCrosstalkCalibration	Man page
plotBasepair	Man page
plotBasepair.AllelicCrosstalkCalibration	Man page
plotBoxplot	Man page
plotBoxplot.ChipEffectSet	Man page
plotBoxplotStats	Man page
plotBoxplotStats.list	Man page
plotCovariateEffects	Man page
plotCovariateEffects.GcContentNormalization2	Man page
plotDensity	Man page
plotDensity,AffymetrixCelFile-method	Man page
plotDensity,AffymetrixCelSet-method	Man page
plotDensity,GenomeInformation-method	Man page
plotDensity.AffymetrixCelFile	Man page
plotDensity.AffymetrixCelSet	Man page
plotDensity.GenomeInformation	Man page
plotImage	Man page
plotImage,AffymetrixCelFile-method	Man page
plotImage.AffymetrixCelFile	Man page
plotMargins	Man page
plotMargins.SpatialReporter	Man page
plotMvsA	Man page
plotMvsA,AffymetrixCelFile-method	Man page
plotMvsA.AffymetrixCelFile	Man page
plotMvsX	Man page
plotMvsX,AffymetrixCelFile-method	Man page
plotMvsX.AffymetrixCelFile	Man page
plotNuse	Man page
plotNuse.QualityAssessmentModel	Man page
plotRle	Man page
plotRle.QualityAssessmentModel	Man page
plotXYCurve	Man page
plotXYCurve.TransformReport	Man page
plotXYCurveLog2	Man page
plotXYCurveLog2.TransformReport	Man page
predictOne	Man page
predictOne.AbstractProbeSequenceNormalization	Man page
predictOne.BaseCountNormalization	Man page
predictOne.LinearModelProbeSequenceNormalization	Man page
predictOne.MatNormalization	Man page
process,AbstractProbeSequenceNormalization-method	Man page
process,AdditiveCovariatesNormalization-method	Man page
process,AllelicCrosstalkCalibration-method	Man page
process,ArrayExplorer-method	Man page
process,BackgroundCorrection-method	Man page
process,ChipEffectGroupMerge-method	Man page
process,DChipQuantileNormalization-method	Man page
process,FragmentEquivalentClassNormalization-method	Man page
process,FragmentLengthNormalization-method	Man page
process,GcContentNormalization-method	Man page
process,GcRmaBackgroundCorrection-method	Man page
process,GenericReporter-method	Man page
process,LimmaBackgroundCorrection-method	Man page
process,MatNormalization-method	Man page
process,MatSmoothing-method	Man page
process,OpticalBackgroundCorrection-method	Man page
process,QuantileNormalization-method	Man page
process,ReseqCrosstalkCalibration-method	Man page
process,RmaBackgroundCorrection-method	Man page
process,ScaleNormalization-method	Man page
process,ScaleNormalization3-method	Man page
process,SpatialReporter-method	Man page
process,UnitTypeScaleNormalization-method	Man page
process.AbstractProbeSequenceNormalization	Man page
process.AdditiveCovariatesNormalization	Man page
process.AlleleSummation	Man page
process.AllelicCrosstalkCalibration	Man page
process.AromaPipeline	Man page
process.ArrayExplorer	Man page
process.BackgroundCorrection	Man page
process.ChipEffectGroupMerge	Man page
process.DChipQuantileNormalization	Man page
process.FragmentEquivalentClassNormalization	Man page
process.FragmentLengthNormalization	Man page
process.GcContentNormalization	Man page
process.GcRmaBackgroundCorrection	Man page
process.GenericReporter	Man page
process.LimmaBackgroundCorrection	Man page
process.MatNormalization	Man page
process.MatSmoothing	Man page
process.OpticalBackgroundCorrection	Man page
process.QuantileNormalization	Man page
process.ReseqCrosstalkCalibration	Man page
process.RmaBackgroundCorrection	Man page
process.ScaleNormalization	Man page
process.ScaleNormalization3	Man page
process.SpatialReporter	Man page
process.SpatialRowColumnNormalization	Man page
process.UnitTypeScaleNormalization	Man page
randomSeed	Man page
range.AffymetrixCelFile	Man page
range.AffymetrixCelSet	Man page
range.CnagCfhFile	Man page
range.CnagCfhSet	Man page
read10K	Man page
read10K.DChipSnpInformation	Man page
read250K	Man page
read250K.DChipSnpInformation	Man page
read250KHg17	Man page
read250KHg17.DChipGenomeInformation	Man page
read50K	Man page
read50K.DChipSnpInformation	Man page
read50KHg17	Man page
read50KHg17.DChipGenomeInformation	Man page
readArrays	Man page
readArrays.AffymetrixAptSummaryFile	Man page
readCdfGroupStrands	Man page Source code
readCfhHeader	Man page
readCfhHeader.default	Man page
readCfhUnits	Man page
readCfhUnits.default	Man page
readCfnHeader	Man page
readCfnHeader.default	Man page
readCfnUnits	Man page
readCfnUnits.default	Man page
readDataFrame.AffymetrixCdfFile	Man page
readDataFrame.AffymetrixCsvGenomeInformation	Man page
readDataFrame.AffymetrixTsvFile	Man page
readDataFrame.AromaUfcFile	Man page
readDataFrame.DChipCdfBinFile	Man page
readDataFrame.DChipGenomeInformation	Man page
readDataFrame.DChipSnpInformation	Man page
readDataFrame.GenomeInformation	Man page
readDataFrame.SnpInformation	Man page
readDataFrame.UflSnpInformation	Man page
readDataFrame.UgpGenomeInformation	Man page
readDataFrame2	Man page
readDataFrame2.AffymetrixProbeTabFile	Man page
readDataUnitChromosomePosition	Man page
readDataUnitChromosomePosition.AffymetrixNetAffxCsvFile	Man page
readDataUnitFragmentLength	Man page
readDataUnitFragmentLength.AffymetrixNetAffxCsvFile	Man page
readGeneAssignments	Man page
readGeneAssignments.AffymetrixNetAffxCsvFile	Man page
readGenomeWideSNP	Man page
readGenomeWideSNP.DChipGenomeInformation	Man page
readHeader.AffymetrixAptSummaryFile	Man page
readMatchScores	Man page
readMatchScores.AromaCellMatchScoreFile	Man page
readMouse430	Man page
readMouse430.DChipGenomeInformation	Man page
readMouse430KenHardwired	Man page
readMouse430KenHardwired.DChipGenomeInformation	Man page
readParameter	Man page
readParameter.CrlmmParametersFile	Man page
readPlasqTypes	Man page
readPlasqTypes.AffymetrixCdfFile	Man page
readPriorsByUnits	Man page
readPriorsByUnits.MultiArrayUnitModel	Man page
readProbesetIds	Man page
readProbesetIds.AffymetrixAptSummaryFile	Man page
readRawData	Man page
readRawData,AffymetrixCelFile-method	Man page
readRawData.AffymetrixCelFile	Man page
readRawData.AffymetrixCnChpFile	Man page
readRawData.AffymetrixPgfFile	Man page
readRawDataRectangle	Man page
readRawDataRectangle.AffymetrixCelFile	Man page
readRawDataRectangle.SpatialReporter	Man page
readSequenceDataFrame	Man page
readSequenceDataFrame.AffymetrixProbeTabFile	Man page
readTableInternal	Man page
readTableInternal.GenomeInformation	Man page
readTableInternal.SnpInformation	Man page
readUnitNames	Man page
readUnitNames.AffymetrixNetAffxCsvFile	Man page
readUnits	Man page
readUnits,AffymetrixCdfFile-method	Man page
readUnits,AffymetrixCelFile-method	Man page
readUnits,CnagCfhFile-method	Man page
readUnits,MultiArrayUnitModel-method	Man page
readUnits,SingleArrayUnitModel-method	Man page
readUnits.AffymetrixCdfFile	Man page
readUnits.AffymetrixCelFile	Man page
readUnits.AffymetrixCelSet	Man page
readUnits.ChipEffectFile	Man page
readUnits.ChipEffectSet	Man page
readUnits.CnChipEffectFile	Man page
readUnits.CnagCfhFile	Man page
readUnits.CnagCfhSet	Man page
readUnits.ExonChipEffectFile	Man page
readUnits.FirmaFile	Man page
readUnits.FirmaSet	Man page
readUnits.MultiArrayUnitModel	Man page
readUnits.ParameterCelFile	Man page
readUnits.ProbeAffinityFile	Man page
readUnits.ResidualFile	Man page
readUnits.ResidualSet	Man page
readUnits.SingleArrayUnitModel	Man page
readUnits.SnpChipEffectFile	Man page
readUnits.WeightsFile	Man page
readUnits.WeightsSet	Man page
readUnitsByQuartets	Man page
readUnitsByQuartets,AffymetrixCdfFile-method	Man page
readUnitsByQuartets.AffymetrixCdfFile	Man page
rescale.AllelicCrosstalkCalibration	Man page
rescaleByAll	Man page
rescaleByAll.AllelicCrosstalkCalibration	Man page
rescaleByAll.ReseqCrosstalkCalibration	Man page
rescaleByGroups	Man page
rescaleByGroups.AllelicCrosstalkCalibration	Man page
restruct	Man page
restruct.AffymetrixCdfFile	Man page
seq.TransformReport	Man page
setAlias,GenericReporter-method	Man page
setAlias,Model-method	Man page
setAlias.ArrayExplorer	Man page
setAlias.GenericReporter	Man page
setAlias.Model	Man page
setAlias.TransformReport	Man page
setArrays,ArrayExplorer-method	Man page
setArrays.ArrayExplorer	Man page
setBandwidth	Man page
setBandwidth.SmoothMultiarrayModel	Man page
setCdf	Man page
setCdf,AffymetrixCelFile-method	Man page
setCdf,AffymetrixCelSet-method	Man page
setCdf,CnagCfhFile-method	Man page
setCdf,CnagCfhSet-method	Man page
setCdf.AffymetrixCelFile	Man page
setCdf.AffymetrixCelSet	Man page
setCdf.AffymetrixCnChpFile	Man page
setCdf.AffymetrixCnChpSet	Man page
setCdf.CnagCfhFile	Man page
setCdf.CnagCfhSet	Man page
setColorMaps	Man page
setColorMaps.ArrayExplorer	Man page
setColorMaps.SpatialReporter	Man page
setCombineAlleles	Man page
setCombineAlleles.CnChipEffectSet	Man page
setCombineAlleles.CnPlm	Man page
setCombineAlleles.CnProbeAffinityFile	Man page
setCustomFindCdf	Man page Source code
setDecodeFunction	Man page
setDecodeFunction.ParameterCelFile	Man page
setEncodeFunction	Man page
setEncodeFunction.ParameterCelFile	Man page
setGenomeInformation	Man page
setGenomeInformation.AffymetrixCdfFile	Man page
setLabel.Model	Man page
setListOfPriors	Man page
setListOfPriors.MultiArrayUnitModel	Man page
setMergeFunction	Man page
setMergeFunction.ChipEffectGroupMerge	Man page
setMergeGroups	Man page
setMergeGroups.ExonChipEffectSet	Man page
setMergeGroups.ExonProbeAffinityFile	Man page
setMergeGroups.ExonRmaPlm	Man page
setMergeStrands	Man page
setMergeStrands.SnpChipEffectSet	Man page
setMergeStrands.SnpPlm	Man page
setMergeStrands.SnpProbeAffinityFile	Man page
setReference.SpatialReporter	Man page
setRestructor	Man page
setRestructor,AffymetrixCdfFile-method	Man page
setRestructor.AffymetrixCdfFile	Man page
setSettings	Man page
setSettings.Package	Man page
setSnpInformation	Man page
setSnpInformation.AffymetrixCdfFile	Man page
setTags,Model-method	Man page
setTags.Model	Man page
setUnitReadMap	Man page
setUnitReadMap.AffymetrixCnChpFile	Man page
setup.GenericReporter	Man page
setupExampleData	Man page
setupExampleData,AromaAffymetrix-method	Man page
setupExampleData.AromaAffymetrix	Man page
smoothScatterMvsA	Man page
smoothScatterMvsA,AffymetrixCelFile-method	Man page
smoothScatterMvsA.AffymetrixCelFile	Man page
stextChipType.AffymetrixCdfFile	Man page
transformAffine	Man page
transformAffine.AffymetrixCelFile	Man page
transformAffine.AffymetrixCelSet	Man page
translateColumnNames.AffymetrixAptSummaryFile	Man page
translateColumnNames.AffymetrixProbeTabFile	Man page
translateColumnNames.AffymetrixTabularFile	Man page
translateFullName.AffymetrixProbeTabFile	Man page
update.AromaAffymetrix	Man page
update2.AffymetrixCelSet	Man page
updateDataFlat	Man page
updateDataFlat.ChipEffectFile	Man page
updateDataFlat.FirmaFile	Man page
updateDataFlat.ResidualFile	Man page
updateDataFlat.WeightsFile	Man page
updateMatchScores	Man page
updateMatchScores.AromaCellMatchScoreFile	Man page
updateParameter	Man page
updateParameter.CrlmmParametersFile	Man page
updateSampleAnnotationSet	Man page
updateSampleAnnotationSet.AffymetrixCelSet	Man page
updateSettings	Man page
updateSettings.Package	Man page
updateSetupExplorerFile.ArrayExplorer	Man page
updateUnits	Man page
updateUnits,AffymetrixCelFile-method	Man page
updateUnits.AffymetrixCelFile	Man page
updateUnits.ChipEffectFile	Man page
updateUnits.ChipEffectSet	Man page
updateUnits.FirmaFile	Man page
updateUnits.FirmaSet	Man page
updateUnits.ParameterCelFile	Man page
updateUnits.ProbeAffinityFile	Man page
updateUnits.ResidualFile	Man page
updateUnits.ResidualSet	Man page
updateUnits.WeightsFile	Man page
updateUnits.WeightsSet	Man page
validate.AffymetrixCdfFile	Man page
validate.AvgPlm	Man page
validate.MultiArrayUnitModel	Man page
verify,GenomeInformation-method	Man page
verify,SnpInformation-method	Man page
verify.AffymetrixCsvGenomeInformation	Man page
verify.AffymetrixTsvFile	Man page
verify.DChipGenomeInformation	Man page
verify.DChipSnpInformation	Man page
verify.GenomeInformation	Man page
verify.SnpInformation	Man page
verify.UflSnpInformation	Man page
verify.UgpGenomeInformation	Man page
writeAsFullCelFile	Man page
writeAsFullCelFile.ChipEffectFile	Man page
writeCNT	Man page
writeCNT.SnpChipEffectFile	Man page
writeCNT.SnpChipEffectSet	Man page
writeCdf	Man page
writeCdf,AffyGenePDInfo-method	Man page
writeCdf.AffyGenePDInfo	Man page
writeCdf.DBPDInfo	Man page
writeCdf.PDInfoList	Man page
writeCdf.default	Man page
writeCdfByExcludingCells	Man page
writeCdfByExcludingCells.AffymetrixCdfFile	Man page
writeImage,AffymetrixCelFile-method	Man page
writeImage.AffymetrixCelFile	Man page
writeImage.ResidualFile	Man page
writeImage.WeightsFile	Man page
writeImageCombined	Man page
writeImageCombined.TransformReport	Man page
writeImages	Man page
writeImages.SpatialReporter	Man page
writeImages.TransformReport	Man page
writeRegions.profileCGH	Man page
writeSgr	Man page
writeSgr.AffymetrixCelSet	Man page
writeSignals	Man page
writeSignals.ProbeLevelTransform3	Man page
writeWig	Man page
writeWig.CnChipEffectSet	Man page