aroma.affymetrix-package	aroma.affymetrix-package
AbstractProbeSequenceNormalization	AbstractProbeSequenceNormalization
AbstractProbeSequenceNormalization.process	process.AbstractProbeSequenceNormalization
addColorMap	Non-documented_objects
addColorMap.ArrayExplorer	Non-documented_objects
addColorMap.SpatialReporter	Non-documented_objects
addExclCells	Non-documented_objects
addExclCells.DChipQuantileNormalization	Non-documented_objects
AdditiveCovariatesNormalization	AdditiveCovariatesNormalization
AdditiveCovariatesNormalization.process	process.AdditiveCovariatesNormalization
AffineCnPlm	AffineCnPlm
AffinePlm	AffinePlm
AffinePlm.getFitUnitGroupFunction	getFitUnitGroupFunction.AffinePlm
AffineSnpPlm	AffineSnpPlm
AffyGenePDInfo.writeCdf	writeCdf.AffyGenePDInfo
AffymetrixAptSummaryFile	Non-documented_objects
AffymetrixCdfFile	AffymetrixCdfFile
AffymetrixCdfFile.compare	compare.AffymetrixCdfFile
AffymetrixCdfFile.computeAffinities	computeAffinities.AffymetrixCdfFile
AffymetrixCdfFile.convert	convert.AffymetrixCdfFile
AffymetrixCdfFile.convertUnits	convertUnits.AffymetrixCdfFile
AffymetrixCdfFile.createExonByTranscriptCdf	createExonByTranscriptCdf.AffymetrixCdfFile
AffymetrixCdfFile.createMonoCell	createMonocellCdf.AffymetrixCdfFile
AffymetrixCdfFile.createMonocellCdf	createMonocellCdf.AffymetrixCdfFile
AffymetrixCdfFile.createUnique	createUniqueCdf.AffymetrixCdfFile
AffymetrixCdfFile.createUniqueCdf	createUniqueCdf.AffymetrixCdfFile
AffymetrixCdfFile.findByChipType	findByChipType.AffymetrixCdfFile
AffymetrixCdfFile.fromFile	fromFile.AffymetrixCdfFile
AffymetrixCdfFile.getAlleleCellPairs	getAlleleCellPairs.AffymetrixCdfFile
AffymetrixCdfFile.getAlleleProbePairs	getAlleleProbePairs.AffymetrixCdfFile
AffymetrixCdfFile.getAlleleProbePairs3	getAlleleProbePairs3.AffymetrixCdfFile
AffymetrixCdfFile.getCellIndices	getCellIndices.AffymetrixCdfFile
AffymetrixCdfFile.getCnNames	getCnNames.AffymetrixCdfFile
AffymetrixCdfFile.getGenomeInformation	getGenomeInformation.AffymetrixCdfFile
AffymetrixCdfFile.getHeader	getHeader.AffymetrixCdfFile
AffymetrixCdfFile.getSnpNames	getSnpNames.AffymetrixCdfFile
AffymetrixCdfFile.getUnitNames	getUnitNames.AffymetrixCdfFile
AffymetrixCdfFile.getUnitSizes	nbrOfGroupsPerUnit.AffymetrixCdfFile
AffymetrixCdfFile.getUnitTypes	getUnitTypes.AffymetrixCdfFile
AffymetrixCdfFile.groupUnitsByDimension	groupUnitsByDimension.AffymetrixCdfFile
AffymetrixCdfFile.isPm	isPm.AffymetrixCdfFile
AffymetrixCdfFile.isResequenceChip	isResequenceChip.AffymetrixCdfFile
AffymetrixCdfFile.isSnpChip	isSnpChip.AffymetrixCdfFile
AffymetrixCdfFile.nbrOfGroupsPerUnit	nbrOfGroupsPerUnit.AffymetrixCdfFile
AffymetrixCdfFile.nbrOfSnps	nbrOfSnps.AffymetrixCdfFile
AffymetrixCdfFile.readUnits	readUnits.AffymetrixCdfFile
AffymetrixCdfFile.readUnitsByQuartets	readUnitsByQuartets.AffymetrixCdfFile
AffymetrixCdfFile.setRestructor	setRestructor.AffymetrixCdfFile
AffymetrixCelFile	AffymetrixCelFile
AffymetrixCelFile.allocateFromCdf	allocateFromCdf.AffymetrixCelFile
AffymetrixCelFile.bgAdjustGcrma	bgAdjustGcrma.AffymetrixCelFile
AffymetrixCelFile.bgAdjustOptical	bgAdjustOptical.AffymetrixCelFile
AffymetrixCelFile.bgAdjustRma	bgAdjustRma.AffymetrixCelFile
AffymetrixCelFile.clearData	clearData.AffymetrixCelFile
AffymetrixCelFile.createFrom	createFrom.AffymetrixCelFile
AffymetrixCelFile.fitQuantileNormFcn	fitQuantileNormFcn.AffymetrixCelFile
AffymetrixCelFile.fromFile	fromFile.AffymetrixCelFile
AffymetrixCelFile.getCdf	getCdf.AffymetrixCelFile
AffymetrixCelFile.getChipType	getChipType.AffymetrixCelFile
AffymetrixCelFile.getData	readRawData.AffymetrixCelFile
AffymetrixCelFile.getHeader	getHeader.AffymetrixCelFile
AffymetrixCelFile.getImage	getImage.AffymetrixCelFile
AffymetrixCelFile.getTimestamp	getTimestamp.AffymetrixCelFile
AffymetrixCelFile.image270	image270.AffymetrixCelFile
AffymetrixCelFile.normalizeQuantile	normalizeQuantile.AffymetrixCelFile
AffymetrixCelFile.plotDensity	plotDensity.AffymetrixCelFile
AffymetrixCelFile.plotImage	plotImage.AffymetrixCelFile
AffymetrixCelFile.plotMvsA	plotMvsA.AffymetrixCelFile
AffymetrixCelFile.plotMvsX	plotMvsX.AffymetrixCelFile
AffymetrixCelFile.readRawData	readRawData.AffymetrixCelFile
AffymetrixCelFile.readUnits	readUnits.AffymetrixCelFile
AffymetrixCelFile.setCdf	setCdf.AffymetrixCelFile
AffymetrixCelFile.smoothScatterMvsA	smoothScatterMvsA.AffymetrixCelFile
AffymetrixCelFile.updateUnits	updateUnits.AffymetrixCelFile
AffymetrixCelFile.writeImage	writeImage.AffymetrixCelFile
AffymetrixCelSet	AffymetrixCelSet
AffymetrixCelSet.as.AffymetrixCelSet	as.AffymetrixCelSet.AffymetrixCelSet
AffymetrixCelSet.as.character	as.character.AffymetrixCelSet
AffymetrixCelSet.averageQuantile	averageQuantile.AffymetrixCelSet
AffymetrixCelSet.bgAdjustGcrma	bgAdjustGcrma.AffymetrixCelSet
AffymetrixCelSet.bgAdjustOptical	bgAdjustOptical.AffymetrixCelSet
AffymetrixCelSet.bgAdjustRma	bgAdjustRma.AffymetrixCelSet
AffymetrixCelSet.calculateParametersGsb	calculateParametersGsb.AffymetrixCelSet
AffymetrixCelSet.doFIRMA	doFIRMA.AffymetrixCelSet
AffymetrixCelSet.extractAffyBatch	extractAffyBatch.AffymetrixCelSet
AffymetrixCelSet.extractMatrix	extractMatrix.AffymetrixCelSet
AffymetrixCelSet.getAverageFile	getAverageFile.AffymetrixCelSet
AffymetrixCelSet.getCdf	getCdf.AffymetrixCelSet
AffymetrixCelSet.getChipType	getChipType.AffymetrixCelSet
AffymetrixCelSet.getIntensities	getIntensities.AffymetrixCelSet
AffymetrixCelSet.getUnitIntensities	getUnitIntensities.AffymetrixCelSet
AffymetrixCelSet.importFromDChip	importFromDChip.AffymetrixCelSet
AffymetrixCelSet.isDuplicated	isDuplicated.AffymetrixCelSet
AffymetrixCelSet.nbrOfArrays	nbrOfArrays.AffymetrixCelSet
AffymetrixCelSet.normalizeQuantile	normalizeQuantile.AffymetrixCelSet
AffymetrixCelSet.plotDensity	plotDensity.AffymetrixCelSet
AffymetrixCelSet.setCdf	setCdf.AffymetrixCelSet
AffymetrixCelSetReporter	AffymetrixCelSetReporter
AffymetrixCelSetReporter.getDataSet	getDataSet.AffymetrixCelSetReporter
AffymetrixCelSetTuple	AffymetrixCelSetTuple
AffymetrixCnChpFile	Non-documented_objects
AffymetrixCnChpSet	AffymetrixCnChpSet
AffymetrixCnChpSet.as.AffymetrixCnChpSet	as.AffymetrixCnChpSet.AffymetrixCnChpSet
AffymetrixCnChpSet.as.character	as.character.AffymetrixCnChpSet
AffymetrixCnChpSet.nbrOfArrays	nbrOfArrays.AffymetrixCnChpSet
AffymetrixCsvFile	Non-documented_objects
AffymetrixCsvGenomeInformation	Non-documented_objects
AffymetrixFile	AffymetrixFile
AffymetrixFileSet	AffymetrixFileSet
AffymetrixFileSet.as.AffymetrixFileSet	as.AffymetrixFileSet.AffymetrixFileSet
AffymetrixFileSet.byPath	byPath.AffymetrixFileSet
AffymetrixFileSetReporter	AffymetrixFileSetReporter
AffymetrixNetAffxCsvFile	Non-documented_objects
AffymetrixPlatform	Non-documented_objects
AffymetrixProbeTabFile	AffymetrixProbeTabFile
AffymetrixTabularFile	Non-documented_objects
AffymetrixTsvFile	Non-documented_objects
AlleleSummation	AlleleSummation
AlleleSummation.getChipEffectSet	getChipEffectSet.AlleleSummation
AllelicCrosstalkCalibration	AllelicCrosstalkCalibration
AllelicCrosstalkCalibration.process	process.AllelicCrosstalkCalibration
allocate.AromaCellMatchScoreFile	Non-documented_objects
allocate.CrlmmParametersFile	Non-documented_objects
allocateFromCdf	Non-documented_objects
allocateFromCdf,AffymetrixCelFile-method	allocateFromCdf.AffymetrixCelFile
allocateFromCdf,AromaUnitTabularBinaryFile-method	allocateFromCdf.AromaUnitTabularBinaryFile
allocateFromCdf.AffymetrixCelFile	allocateFromCdf.AffymetrixCelFile
allocateFromCdf.AromaCellCpgFile	Non-documented_objects
allocateFromCdf.AromaCellMatchScoreFile	Non-documented_objects
allocateFromCdf.AromaCellPositionFile	Non-documented_objects
allocateFromCdf.AromaCellSequenceFile	Non-documented_objects
allocateFromCdf.AromaUfcFile	Non-documented_objects
allocateFromCdf.AromaUflFile	Non-documented_objects
allocateFromCdf.AromaUnitGcContentFile	Non-documented_objects
allocateFromCdf.AromaUnitTabularBinaryFile	allocateFromCdf.AromaUnitTabularBinaryFile
annotateMvsA	Non-documented_objects
annotateMvsA.AffymetrixCelFile	Non-documented_objects
append	Non-documented_objects
append.AffymetrixCelSet	Non-documented_objects
append.CnagCfhSet	Non-documented_objects
apply	Non-documented_objects
applyAnyOrder	Non-documented_objects
applyAnyOrder.CopyNumberChromosomalModel	Non-documented_objects
applyCCF0	Non-documented_objects
applyCCF0.CopyNumberChromosomalModel	Non-documented_objects
applyCFC0	Non-documented_objects
applyCFC0.CopyNumberChromosomalModel	Non-documented_objects
applyToUnitIntensities	Non-documented_objects
applyToUnitIntensities.AffymetrixCelSet	Non-documented_objects
aroma.affymetrix	aroma.affymetrix-package
AromaAffymetrix	Non-documented_objects
AromaCellMatchScoreFile	Non-documented_objects
AromaChipTypeAnnotationFile	AromaChipTypeAnnotationFile
AromaChipTypeAnnotationFile.byChipType	byChipType.AromaChipTypeAnnotationFile
AromaChipTypeAnnotationFile.byName	byChipType.AromaChipTypeAnnotationFile
AromaChipTypeAnnotationFile.findByChipType	findByChipType.AromaChipTypeAnnotationFile
AromaChipTypeAnnotationFile.fromFile	fromFile.AromaChipTypeAnnotationFile
AromaChipTypeAnnotationFile.getHeader	getHeader.AromaChipTypeAnnotationFile
AromaPipeline	Non-documented_objects
AromaUfcFile	Non-documented_objects
AromaUgcFile	Non-documented_objects
AromaUnitGcContentFile	Non-documented_objects
AromaUnitTabularBinaryFile.allocateFromCdf	allocateFromCdf.AromaUnitTabularBinaryFile
ArrayExplorer	ArrayExplorer
ArrayExplorer.getDataSet	getDataSet.ArrayExplorer
ArrayExplorer.process	process.ArrayExplorer
ArrayExplorer.setArrays	setArrays.ArrayExplorer
as.AffymetrixCelSet	Non-documented_objects
as.AffymetrixCelSet,AffymetrixCelSet-method	as.AffymetrixCelSet.AffymetrixCelSet
as.AffymetrixCelSet.AffymetrixCelSet	as.AffymetrixCelSet.AffymetrixCelSet
as.AffymetrixCelSet.default	as.AffymetrixCelSet.AffymetrixCelSet
as.AffymetrixCelSet.list	as.AffymetrixCelSet.AffymetrixCelSet
as.AffymetrixCnChpSet	Non-documented_objects
as.AffymetrixCnChpSet,AffymetrixCnChpSet-method	as.AffymetrixCnChpSet.AffymetrixCnChpSet
as.AffymetrixCnChpSet.AffymetrixCnChpSet	as.AffymetrixCnChpSet.AffymetrixCnChpSet
as.AffymetrixCnChpSet.default	as.AffymetrixCnChpSet.AffymetrixCnChpSet
as.AffymetrixCnChpSet.list	as.AffymetrixCnChpSet.AffymetrixCnChpSet
as.AffymetrixFileSet	Non-documented_objects
as.AffymetrixFileSet,AffymetrixFileSet-method	as.AffymetrixFileSet.AffymetrixFileSet
as.AffymetrixFileSet.AffymetrixFileSet	as.AffymetrixFileSet.AffymetrixFileSet
as.AffymetrixFileSet.default	as.AffymetrixFileSet.AffymetrixFileSet
as.AffymetrixFileSet.list	as.AffymetrixFileSet.AffymetrixFileSet
as.character,AffymetrixCelSet-method	as.character.AffymetrixCelSet
as.character,AffymetrixCnChpSet-method	as.character.AffymetrixCnChpSet
as.character,CnagCfhSet-method	as.character.CnagCfhSet
as.character,DChipDcpSet-method	as.character.DChipDcpSet
as.character.AffymetrixCdfFile	Non-documented_objects
as.character.AffymetrixCelFile	Non-documented_objects
as.character.AffymetrixCelSet	as.character.AffymetrixCelSet
as.character.AffymetrixCelSetReporter	Non-documented_objects
as.character.AffymetrixCnChpFile	Non-documented_objects
as.character.AffymetrixCnChpSet	as.character.AffymetrixCnChpSet
as.character.AffymetrixProbeTabFile	Non-documented_objects
as.character.AromaChipTypeAnnotationFile	Non-documented_objects
as.character.ArrayExplorer	Non-documented_objects
as.character.ChipEffectFile	Non-documented_objects
as.character.ChipEffectSet	Non-documented_objects
as.character.CnagCfhFile	Non-documented_objects
as.character.CnagCfhSet	as.character.CnagCfhSet
as.character.DChipCdfBinFile	Non-documented_objects
as.character.DChipDcpFile	Non-documented_objects
as.character.DChipDcpSet	as.character.DChipDcpSet
as.character.DChipQuantileNormalization	Non-documented_objects
as.character.FirmaModel	Non-documented_objects
as.character.GenericReporter	Non-documented_objects
as.character.GenomeInformation	Non-documented_objects
as.character.Model	Non-documented_objects
as.character.ProbeAffinityFile	Non-documented_objects
as.character.QualityAssessmentModel	Non-documented_objects
as.character.ResidualFile	Non-documented_objects
as.character.ResidualSet	Non-documented_objects
as.character.SmoothMultiarrayModel	Non-documented_objects
as.character.SnpInformation	Non-documented_objects
as.character.SpatialReporter	Non-documented_objects
as.character.TransformReport	Non-documented_objects
as.character.WeightsFile	Non-documented_objects
as.character.WeightsSet	Non-documented_objects
as.ChipEffectSetTuple	Non-documented_objects
as.ChipEffectSetTuple.ChipEffectSetTuple	Non-documented_objects
as.ChipEffectSetTuple.default	Non-documented_objects
as.CnagCfhSet	Non-documented_objects
as.CnagCfhSet,CnagCfhSet-method	as.CnagCfhSet.CnagCfhSet
as.CnagCfhSet.CnagCfhSet	as.CnagCfhSet.CnagCfhSet
as.CnagCfhSet.default	as.CnagCfhSet.CnagCfhSet
as.CnagCfhSet.list	as.CnagCfhSet.CnagCfhSet
as.CnChipEffectSetTuple	Non-documented_objects
as.CnChipEffectSetTuple.CnChipEffectSetTuple	Non-documented_objects
as.CnChipEffectSetTuple.default	Non-documented_objects
as.CopyNumberDataSetTuple.CnChipEffectSet	Non-documented_objects
as.DChipDcpSet	Non-documented_objects
as.DChipDcpSet,DChipDcpSet-method	as.DChipDcpSet.DChipDcpSet
as.DChipDcpSet.DChipDcpSet	as.DChipDcpSet.DChipDcpSet
as.DChipDcpSet.default	as.DChipDcpSet.DChipDcpSet
as.DChipDcpSet.list	as.DChipDcpSet.DChipDcpSet
ASCRMAv2	Non-documented_objects
assertAnnotationData	Non-documented_objects
assertAnnotationData.ASCRMAv2	Non-documented_objects
averageQuantile,AffymetrixCelSet-method	averageQuantile.AffymetrixCelSet
averageQuantile.AffymetrixCelSet	averageQuantile.AffymetrixCelSet
AvgCnPlm	AvgCnPlm
AvgPlm	AvgPlm
AvgPlm.getFitUnitGroupFunction	getFitUnitGroupFunction.AvgPlm
AvgSnpPlm	AvgSnpPlm
BackgroundCorrection	BackgroundCorrection
BackgroundCorrection.process	process.BackgroundCorrection
BaseCountNormalization	BaseCountNormalization
BasePositionNormalization	BasePositionNormalization
bgAdjustGcrma	Non-documented_objects
bgAdjustGcrma,AffymetrixCelFile-method	bgAdjustGcrma.AffymetrixCelFile
bgAdjustGcrma,AffymetrixCelSet-method	bgAdjustGcrma.AffymetrixCelSet
bgAdjustGcrma.AffymetrixCelFile	bgAdjustGcrma.AffymetrixCelFile
bgAdjustGcrma.AffymetrixCelSet	bgAdjustGcrma.AffymetrixCelSet
bgAdjustOptical	Non-documented_objects
bgAdjustOptical,AffymetrixCelFile-method	bgAdjustOptical.AffymetrixCelFile
bgAdjustOptical,AffymetrixCelSet-method	bgAdjustOptical.AffymetrixCelSet
bgAdjustOptical.AffymetrixCelFile	bgAdjustOptical.AffymetrixCelFile
bgAdjustOptical.AffymetrixCelSet	bgAdjustOptical.AffymetrixCelSet
bgAdjustRma	Non-documented_objects
bgAdjustRma,AffymetrixCelFile-method	bgAdjustRma.AffymetrixCelFile
bgAdjustRma,AffymetrixCelSet-method	bgAdjustRma.AffymetrixCelSet
bgAdjustRma.AffymetrixCelFile	bgAdjustRma.AffymetrixCelFile
bgAdjustRma.AffymetrixCelSet	bgAdjustRma.AffymetrixCelSet
boxplot.stats	Non-documented_objects
boxplotStats	Non-documented_objects
boxplotStats.ChipEffectSet	Non-documented_objects
bpmapCluster2Cdf	bpmapCluster2Cdf
bpmapCluster2Cdf.default	bpmapCluster2Cdf
byChipType,AromaChipTypeAnnotationFile-method	byChipType.AromaChipTypeAnnotationFile
byChipType,DChipGenomeInformation-method	byChipType.DChipGenomeInformation
byChipType,DChipSnpInformation-method	byChipType.DChipSnpInformation
byChipType,GenomeInformation-method	byChipType.GenomeInformation
byChipType,SnpInformation-method	byChipType.SnpInformation
byChipType,UgpGenomeInformation-method	byChipType.UgpGenomeInformation
byChipType.AffymetrixCsvGenomeInformation	Non-documented_objects
byChipType.AffymetrixProbeTabFile	Non-documented_objects
byChipType.AffymetrixTabularFile	Non-documented_objects
byChipType.AffymetrixTsvFile	Non-documented_objects
byChipType.AromaCellMatchScoreFile	Non-documented_objects
byChipType.AromaChipTypeAnnotationFile	byChipType.AromaChipTypeAnnotationFile
byChipType.DChipCdfBinFile	Non-documented_objects
byChipType.DChipGenomeInformation	byChipType.DChipGenomeInformation
byChipType.DChipSnpInformation	byChipType.DChipSnpInformation
byChipType.GenomeInformation	byChipType.GenomeInformation
byChipType.SnpInformation	byChipType.SnpInformation
byChipType.UflSnpInformation	Non-documented_objects
byChipType.UgpGenomeInformation	byChipType.UgpGenomeInformation
byName,AromaChipTypeAnnotationFile-method	byChipType.AromaChipTypeAnnotationFile
byName.AffymetrixCelSet	Non-documented_objects
byName.AffymetrixCnChpSet	Non-documented_objects
byName.AromaChipTypeAnnotationFile	byChipType.AromaChipTypeAnnotationFile
byName.CnagCfhSet	Non-documented_objects
byName.CrlmmParametersSet	Non-documented_objects
byName.DChipDcpSet	Non-documented_objects
byPath,AffymetrixFileSet-method	byPath.AffymetrixFileSet
byPath.AffymetrixCelSet	Non-documented_objects
byPath.AffymetrixCelSetTuple	Non-documented_objects
byPath.AffymetrixCnChpSet	Non-documented_objects
byPath.AffymetrixFileSet	byPath.AffymetrixFileSet
byPath.ChipEffectSet	Non-documented_objects
byPath.CnagCfhSet	Non-documented_objects
byPath.CnChipEffectSet	Non-documented_objects
byPath.CrlmmParametersSet	Non-documented_objects
byPath.DChipDcpSet	Non-documented_objects
byPath.ExonChipEffectSet	Non-documented_objects
byPath.FirmaSet	Non-documented_objects
byPath.ResidualSet	Non-documented_objects
byPath.SnpChipEffectSet	Non-documented_objects
byPath.WeightsSet	Non-documented_objects
calcRawCnStats	Non-documented_objects
calcRawCnStats.CopyNumberChromosomalModel	Non-documented_objects
calcRawCnStats.default	Non-documented_objects
calculateAverages	Non-documented_objects
calculateAverages.FragmentEquivalentClassNormalization	Non-documented_objects
calculateBaseline	Non-documented_objects
calculateBaseline,ChipEffectSet-method	calculateBaseline.ChipEffectSet
calculateBaseline.ChipEffectSet	calculateBaseline.ChipEffectSet
calculateConfidenceScores	Non-documented_objects
calculateConfidenceScores.CrlmmModel	Non-documented_objects
calculateFieldBoxplotStats	Non-documented_objects
calculateFieldBoxplotStats.ChipEffectSet	Non-documented_objects
calculateMargins	Non-documented_objects
calculateMargins.SpatialReporter	Non-documented_objects
calculateNuseBoxplotStats	Non-documented_objects
calculateNuseBoxplotStats.ChipEffectSet	Non-documented_objects
calculateParametersGsb	Non-documented_objects
calculateParametersGsb,AffymetrixCelSet-method	calculateParametersGsb.AffymetrixCelSet
calculateParametersGsb.AffymetrixCelSet	calculateParametersGsb.AffymetrixCelSet
calculateResiduals	Non-documented_objects
calculateResiduals,FirmaModel-method	calculateResidualSet.FirmaModel
calculateResiduals.FirmaModel	calculateResidualSet.FirmaModel
calculateResiduals.ProbeLevelModel	Non-documented_objects
calculateResidualSet	Non-documented_objects
calculateResidualSet,FirmaModel-method	calculateResidualSet.FirmaModel
calculateResidualSet.FirmaModel	calculateResidualSet.FirmaModel
calculateResidualSet.ProbeLevelModel	Non-documented_objects
calculateRleBoxplotStats	Non-documented_objects
calculateRleBoxplotStats.ChipEffectSet	Non-documented_objects
calculateTargetDistribution	Non-documented_objects
calculateTargetDistribution.QuantileNormalization	Non-documented_objects
calculateWeights	Non-documented_objects
calculateWeights.ExonRmaPlm	Non-documented_objects
calculateWeights.FirmaModel	Non-documented_objects
calculateWeights.ProbeLevelModel	Non-documented_objects
calibrateOne	Non-documented_objects
calibrateOne.ReseqCrosstalkCalibration	Non-documented_objects
cat	Non-documented_objects
cdfMergeGroups	Non-documented_objects
ChipEffectFile	ChipEffectFile
ChipEffectFile.fromDataFile	fromDataFile.ChipEffectFile
ChipEffectFile.getAM	getAM.ChipEffectFile
ChipEffectFile.getCellMap	getUnitGroupCellMap.ChipEffectFile
ChipEffectFile.getUnitGroupCellMap	getUnitGroupCellMap.ChipEffectFile
ChipEffectFile.getXAM	getXAM.ChipEffectFile
ChipEffectGroupMerge	ChipEffectGroupMerge
ChipEffectGroupMerge.process	process.ChipEffectGroupMerge
ChipEffectSet	ChipEffectSet
ChipEffectSet.calculateBaseline	calculateBaseline.ChipEffectSet
ChipEffectSet.extractExpressionSet	extractExpressionSet.ChipEffectSet
ChipEffectSet.getAM	getAM.ChipEffectSet
ChipEffectSet.getBaseline	getBaseline.ChipEffectSet
ChipEffectSet.getXAM	getXAM.ChipEffectSet
ChipEffectSetTuple	Non-documented_objects
ChipEffectTransform	ChipEffectTransform
clearCache.AdditiveCovariatesNormalization	Non-documented_objects
clearCache.AffymetrixCdfFile	Non-documented_objects
clearCache.AffymetrixCelFile	Non-documented_objects
clearCache.AffymetrixCelSet	Non-documented_objects
clearCache.AffymetrixCnChpFile	Non-documented_objects
clearCache.AffymetrixNetAffxCsvFile	Non-documented_objects
clearCache.AffymetrixProbeTabFile	Non-documented_objects
clearCache.AffymetrixTsvFile	Non-documented_objects
clearCache.AllelicCrosstalkCalibration	Non-documented_objects
clearCache.ChipEffectFile	Non-documented_objects
clearCache.ChipEffectSet	Non-documented_objects
clearCache.CnagCfhFile	Non-documented_objects
clearCache.CnagCfhSet	Non-documented_objects
clearCache.DChipCdfBinFile	Non-documented_objects
clearCache.ExonChipEffectFile	Non-documented_objects
clearCache.FirmaFile	Non-documented_objects
clearCache.FirmaModel	Non-documented_objects
clearCache.FirmaSet	Non-documented_objects
clearCache.FragmentEquivalentClassNormalization	Non-documented_objects
clearCache.FragmentLengthNormalization	Non-documented_objects
clearCache.GenomeInformation	Non-documented_objects
clearCache.ParameterCelFile	Non-documented_objects
clearCache.ProbeAffinityFile	Non-documented_objects
clearCache.ProbeLevelModel	Non-documented_objects
clearCache.ProbeLevelTransform3	Non-documented_objects
clearCache.QualityAssessmentFile	Non-documented_objects
clearCache.QuantileNormalization	Non-documented_objects
clearCache.ReseqCrosstalkCalibration	Non-documented_objects
clearCache.ResidualFile	Non-documented_objects
clearCache.ResidualSet	Non-documented_objects
clearCache.SmoothMultiarrayModel	Non-documented_objects
clearCache.SnpChipEffectFile	Non-documented_objects
clearCache.SnpInformation	Non-documented_objects
clearCache.TransformReport	Non-documented_objects
clearCache.UgpGenomeInformation	Non-documented_objects
clearCache.WeightsFile	Non-documented_objects
clearCache.WeightsSet	Non-documented_objects
clearData	Non-documented_objects
clearData,AffymetrixCelFile-method	clearData.AffymetrixCelFile
clearData.AffymetrixCelFile	clearData.AffymetrixCelFile
clone.AffymetrixCelFile	Non-documented_objects
clone.AffymetrixCelSet	Non-documented_objects
clone.AffymetrixCnChpFile	Non-documented_objects
clone.CnagCfhFile	Non-documented_objects
clone.CnagCfhSet	Non-documented_objects
CnagCfhFile	CnagCfhFile
CnagCfhFile.fromFile	fromFile.CnagCfhFile
CnagCfhFile.getCdf	getCdf.CnagCfhFile
CnagCfhFile.getChipType	getChipType.CnagCfhFile
CnagCfhFile.getHeader	getHeader.CnagCfhFile
CnagCfhFile.readUnits	readUnits.CnagCfhFile
CnagCfhFile.setCdf	setCdf.CnagCfhFile
CnagCfhSet	CnagCfhSet
CnagCfhSet.as.character	as.character.CnagCfhSet
CnagCfhSet.as.CnagCfhSet	as.CnagCfhSet.CnagCfhSet
CnagCfhSet.getAverageFile	getAverageFile.CnagCfhSet
CnagCfhSet.getCdf	getCdf.CnagCfhSet
CnagCfhSet.isDuplicated	isDuplicated.CnagCfhSet
CnagCfhSet.nbrOfArrays	nbrOfArrays.CnagCfhSet
CnagCfhSet.setCdf	setCdf.CnagCfhSet
CnChipEffectFile	CnChipEffectFile
CnChipEffectSet	CnChipEffectSet
CnChipEffectSet.importFromApt	importFromApt.CnChipEffectSet
CnChipEffectSet.importFromDChip	importFromDChip.CnChipEffectSet
CnChipEffectSetTuple	Non-documented_objects
CnPlm	CnPlm
CnProbeAffinityFile	CnProbeAffinityFile
colMeans	Non-documented_objects
colSums	Non-documented_objects
compare	Non-documented_objects
compare,AffymetrixCdfFile-method	compare.AffymetrixCdfFile
compare.AffymetrixCdfFile	compare.AffymetrixCdfFile
computeAffinities	Non-documented_objects
computeAffinities,AffymetrixCdfFile-method	computeAffinities.AffymetrixCdfFile
computeAffinities.AffymetrixCdfFile	computeAffinities.AffymetrixCdfFile
computeAffinitiesByACS	Non-documented_objects
computeAffinitiesByACS.AffymetrixCdfFile	Non-documented_objects
convert	Non-documented_objects
convert,AffymetrixCdfFile-method	convert.AffymetrixCdfFile
convert.AffymetrixCdfFile	convert.AffymetrixCdfFile
convertToUnique	Non-documented_objects
convertToUnique.AffymetrixCelSet	Non-documented_objects
convertUnits	Non-documented_objects
convertUnits,AffymetrixCdfFile-method	convertUnits.AffymetrixCdfFile
convertUnits.AffymetrixCdfFile	convertUnits.AffymetrixCdfFile
createExonByTranscriptCdf	Non-documented_objects
createExonByTranscriptCdf,AffymetrixCdfFile-method	createExonByTranscriptCdf.AffymetrixCdfFile
createExonByTranscriptCdf.AffymetrixCdfFile	createExonByTranscriptCdf.AffymetrixCdfFile
createFrom	Non-documented_objects
createFrom,AffymetrixCelFile-method	createFrom.AffymetrixCelFile
createFrom.AffymetrixCelFile	createFrom.AffymetrixCelFile
createMonoCell	Non-documented_objects
createMonoCell,AffymetrixCdfFile-method	createMonocellCdf.AffymetrixCdfFile
createMonoCell.AffymetrixCdfFile	createMonocellCdf.AffymetrixCdfFile
createMonocellCdf	Non-documented_objects
createMonocellCdf,AffymetrixCdfFile-method	createMonocellCdf.AffymetrixCdfFile
createMonocellCdf.AffymetrixCdfFile	createMonocellCdf.AffymetrixCdfFile
createOutputTuple	Non-documented_objects
createOutputTuple.SmoothMultiarrayModel	Non-documented_objects
createParamCdf	Non-documented_objects
createParamCdf.ChipEffectFile	Non-documented_objects
createParamCdf.FirmaFile	Non-documented_objects
createUnique	Non-documented_objects
createUnique,AffymetrixCdfFile-method	createUniqueCdf.AffymetrixCdfFile
createUnique.AffymetrixCdfFile	createUniqueCdf.AffymetrixCdfFile
createUniqueCdf	Non-documented_objects
createUniqueCdf,AffymetrixCdfFile-method	createUniqueCdf.AffymetrixCdfFile
createUniqueCdf.AffymetrixCdfFile	createUniqueCdf.AffymetrixCdfFile
CrlmmModel	Non-documented_objects
CrlmmParametersFile	CrlmmParametersFile
CrlmmParametersSet	CrlmmParametersSet
DChipCdfBinFile	DChipCdfBinFile
DChipDcpFile	DChipDcpFile
DChipDcpSet	DChipDcpSet
DChipDcpSet.as.character	as.character.DChipDcpSet
DChipDcpSet.as.DChipDcpSet	as.DChipDcpSet.DChipDcpSet
DChipDcpSet.nbrOfArrays	nbrOfArrays.DChipDcpSet
DChipGenomeInformation	DChipGenomeInformation
DChipGenomeInformation.byChipType	byChipType.DChipGenomeInformation
DChipQuantileNormalization	DChipQuantileNormalization
DChipQuantileNormalization.process	process.DChipQuantileNormalization
DChipSnpInformation	DChipSnpInformation
DChipSnpInformation.byChipType	byChipType.DChipSnpInformation
decode	Non-documented_objects
decode.ParameterCelFile	Non-documented_objects
dim.DChipDcpFile	Non-documented_objects
doASCRMAv1	Non-documented_objects
doASCRMAv1.default	Non-documented_objects
doASCRMAv2	Non-documented_objects
doASCRMAv2.default	Non-documented_objects
doCRMA	Non-documented_objects
doCRMA.default	Non-documented_objects
doCRMAv1	Non-documented_objects
doCRMAv1.AffymetrixCelSet	Non-documented_objects
doCRMAv1.character	Non-documented_objects
doCRMAv2	Non-documented_objects
doCRMAv2.AffymetrixCelSet	Non-documented_objects
doCRMAv2.character	Non-documented_objects
doFIRMA	doFIRMA.AffymetrixCelSet
doFIRMA,AffymetrixCelSet-method	doFIRMA.AffymetrixCelSet
doFIRMA.AffymetrixCelSet	doFIRMA.AffymetrixCelSet
doFIRMA.character	doFIRMA.AffymetrixCelSet
doGCRMA	Non-documented_objects
doGCRMA.AffymetrixCelSet	Non-documented_objects
doGCRMA.character	Non-documented_objects
doRMA	Non-documented_objects
doRMA.AffymetrixCelSet	Non-documented_objects
doRMA.character	Non-documented_objects
dropCellsFromCdfList	Non-documented_objects
encode	Non-documented_objects
encode.ParameterCelFile	Non-documented_objects
Env2Cdf	Non-documented_objects
env2Cdf	Non-documented_objects
excludeChrXFromFit	Non-documented_objects
excludeChrXFromFit.DChipQuantileNormalization	Non-documented_objects
ExonChipEffectFile	ExonChipEffectFile
ExonChipEffectSet	ExonChipEffectSet
ExonProbeAffinityFile	ExonProbeAffinityFile
ExonRmaPlm	ExonRmaPlm
ExonRmaPlm.getFitUnitGroupFunction	getFitUnitGroupFunction.ExonRmaPlm
exportAromaSignalBinaryFileList	Non-documented_objects
exportAromaSignalBinaryFileList.CnChipEffectFile	Non-documented_objects
exportTotalAndFracB	Non-documented_objects
exportTotalAndFracB.CnChipEffectFile	Non-documented_objects
exportTotalAndFracB.CnChipEffectSet	Non-documented_objects
exportTotalAndFracB.DChipDcpSet	Non-documented_objects
exportTotalAndFracB.SnpChipEffectFile	Non-documented_objects
exportTotalAndFracB.SnpChipEffectSet	Non-documented_objects
exportTotalCnRatioSet.AffymetrixCnChpSet	Non-documented_objects
extractAffyBatch	Non-documented_objects
extractAffyBatch,AffymetrixCelSet-method	extractAffyBatch.AffymetrixCelSet
extractAffyBatch.AffymetrixCelSet	extractAffyBatch.AffymetrixCelSet
extractAffyBatch.ChipEffectSet	Non-documented_objects
extractAlleleSet	Non-documented_objects
extractAlleleSet.SnpChipEffectSet	Non-documented_objects
extractChromosomalDataFrame	Non-documented_objects
extractChromosomalDataFrame.ChipEffectFile	Non-documented_objects
extractChromosomalDataFrame.ChipEffectSet	Non-documented_objects
extractCNT	Non-documented_objects
extractCNT.SnpChipEffectFile	Non-documented_objects
extractCNT.SnpChipEffectSet	Non-documented_objects
extractDataFrame	Non-documented_objects
extractDataFrame,ParameterCelSet-method	extractDataFrame.ParameterCelSet
extractDataFrame.ParameterCelFile	Non-documented_objects
extractDataFrame.ParameterCelSet	extractDataFrame.ParameterCelSet
extractExpressionSet	Non-documented_objects
extractExpressionSet,ChipEffectSet-method	extractExpressionSet.ChipEffectSet
extractExpressionSet.ChipEffectSet	extractExpressionSet.ChipEffectSet
extractLogRatios	Non-documented_objects
extractLogRatios.AffymetrixCnChpFile	Non-documented_objects
extractLogRatios.AffymetrixCnChpSet	Non-documented_objects
extractMatrix,AffymetrixCelSet-method	extractMatrix.AffymetrixCelSet
extractMatrix,ParameterCelSet-method	extractMatrix.ParameterCelSet
extractMatrix.AffymetrixCelFile	Non-documented_objects
extractMatrix.AffymetrixCelSet	extractMatrix.AffymetrixCelSet
extractMatrix.ChipEffectFile	Non-documented_objects
extractMatrix.ChipEffectSet	Non-documented_objects
extractMatrix.FirmaFile	Non-documented_objects
extractMatrix.FirmaSet	Non-documented_objects
extractMatrix.ParameterCelFile	Non-documented_objects
extractMatrix.ParameterCelSet	extractMatrix.ParameterCelSet
extractSnpCnvQSet	Non-documented_objects
extractSnpCnvQSet.SnpChipEffectSet	Non-documented_objects
extractSnpFeatureSet	Non-documented_objects
extractSnpFeatureSet.AffymetrixCelSet	Non-documented_objects
extractSnpQSet	Non-documented_objects
extractSnpQSet.SnpChipEffectSet	Non-documented_objects
extractTheta	Non-documented_objects
extractTheta.ChipEffectFile	Non-documented_objects
extractTheta.ChipEffectSet	Non-documented_objects
extractTheta.CnChipEffectFile	Non-documented_objects
extractTheta.CnChipEffectSet	Non-documented_objects
extractTheta.DChipDcpFile	Non-documented_objects
extractTheta.DChipDcpSet	Non-documented_objects
extractTheta.SnpChipEffectFile	Non-documented_objects
extractTheta.SnpChipEffectSet	Non-documented_objects
extractTheta.SnpCnvQSet	Non-documented_objects
extractTheta.SnpQSet	Non-documented_objects
extractTotalAndFracB	Non-documented_objects
extractTotalAndFracB.SnpChipEffectFile	Non-documented_objects
extractTotalAndFreqB	Non-documented_objects
extractTotalAndFreqB.CnChipEffectFile	Non-documented_objects
extractTotalAndFreqB.CnChipEffectSet	Non-documented_objects
extractTotalAndFreqB.default	Non-documented_objects
extractTotalAndFreqB.SnpChipEffectSet	Non-documented_objects
findByCdf2	Non-documented_objects
findByCdf2.default	Non-documented_objects
findByChipType,AffymetrixCdfFile-method	findByChipType.AffymetrixCdfFile
findByChipType,AromaChipTypeAnnotationFile-method	findByChipType.AromaChipTypeAnnotationFile
findByChipType.AffymetrixCdfFile	findByChipType.AffymetrixCdfFile
findByChipType.AffymetrixCsvFile	Non-documented_objects
findByChipType.AffymetrixCsvGenomeInformation	Non-documented_objects
findByChipType.AffymetrixNetAffxCsvFile	Non-documented_objects
findByChipType.AffymetrixProbeTabFile	Non-documented_objects
findByChipType.AffymetrixTabularFile	Non-documented_objects
findByChipType.AffymetrixTsvFile	Non-documented_objects
findByChipType.AromaChipTypeAnnotationFile	findByChipType.AromaChipTypeAnnotationFile
findByChipType.DChipCdfBinFile	Non-documented_objects
findByChipType.DChipGenomeInformation	Non-documented_objects
findByChipType.DChipSnpInformation	Non-documented_objects
findByChipType.UflSnpInformation	Non-documented_objects
findByChipType.UgpGenomeInformation	Non-documented_objects
findByName.AffymetrixCelSet	Non-documented_objects
findByName.AffymetrixCnChpSet	Non-documented_objects
findByName.ChipEffectSet	Non-documented_objects
findByName.CnagCfhSet	Non-documented_objects
findByName.DChipDcpSet	Non-documented_objects
findTargetDistributionFile	Non-documented_objects
findTargetDistributionFile.QuantileNormalization	Non-documented_objects
findUnitsTodo,FirmaModel-method	findUnitsTodo.FirmaModel
findUnitsTodo,ProbeLevelModel-method	findUnitsTodo.ProbeLevelModel
findUnitsTodo,UnitModel-method	findUnitsTodo.UnitModel
findUnitsTodo.AlleleSummation	Non-documented_objects
findUnitsTodo.ChipEffectFile	Non-documented_objects
findUnitsTodo.ChipEffectSet	Non-documented_objects
findUnitsTodo.CrlmmModel	Non-documented_objects
findUnitsTodo.CrlmmParametersFile	Non-documented_objects
findUnitsTodo.CrlmmParametersSet	Non-documented_objects
findUnitsTodo.ExonChipEffectSet	Non-documented_objects
findUnitsTodo.FirmaFile	Non-documented_objects
findUnitsTodo.FirmaModel	findUnitsTodo.FirmaModel
findUnitsTodo.FirmaSet	Non-documented_objects
findUnitsTodo.ProbeLevelModel	findUnitsTodo.ProbeLevelModel
findUnitsTodo.QualityAssessmentFile	Non-documented_objects
findUnitsTodo.ResidualFile	Non-documented_objects
findUnitsTodo.ResidualSet	Non-documented_objects
findUnitsTodo.UnitModel	findUnitsTodo.UnitModel
findUnitsTodo.WeightsFile	Non-documented_objects
findUnitsTodo.WeightsSet	Non-documented_objects
FirmaFile	FirmaFile
FirmaModel	FirmaModel
FirmaModel.calculateResiduals	calculateResidualSet.FirmaModel
FirmaModel.calculateResidualSet	calculateResidualSet.FirmaModel
FirmaModel.findUnitsTodo	findUnitsTodo.FirmaModel
FirmaModel.fit	fit.FirmaModel
FirmaModel.getFirmaScores	getFirmaSet.FirmaModel
FirmaModel.getFirmaSet	getFirmaSet.FirmaModel
FirmaModel.getFitUnitGroupFunction	getFitUnitGroupFunction.FirmaModel
FirmaSet	FirmaSet
fit,FirmaModel-method	fit.FirmaModel
fit,Model-method	fit.Model
fit,ProbeLevelModel-method	fit.ProbeLevelModel
fit,SingleArrayUnitModel-method	fit.SingleArrayUnitModel
fit,SmoothMultiarrayModel-method	fit.SmoothMultiarrayModel
fit.CrlmmModel	Non-documented_objects
fit.FirmaModel	fit.FirmaModel
fit.Model	fit.Model
fit.ProbeLevelModel	fit.ProbeLevelModel
fit.SingleArrayUnitModel	fit.SingleArrayUnitModel
fit.SmoothMultiarrayModel	fit.SmoothMultiarrayModel
fitCnProbes	Non-documented_objects
fitCnProbes.UnitModel	Non-documented_objects
fitOne	Non-documented_objects
fitOne.AbstractProbeSequenceNormalization	Non-documented_objects
fitOne.BaseCountNormalization	Non-documented_objects
fitOne.LinearModelProbeSequenceNormalization	Non-documented_objects
fitOne.MatNormalization	Non-documented_objects
fitOne.ReseqCrosstalkCalibration	Non-documented_objects
fitOne.ScaleNormalization3	Non-documented_objects
fitOne.UnitTypeScaleNormalization	Non-documented_objects
fitOneArray	Non-documented_objects
fitOneArray.SingleArrayUnitModel	Non-documented_objects
fitOneChromosome	Non-documented_objects
fitOneChromosome.SmoothMultiarrayModel	Non-documented_objects
fitPlasqUnit	Non-documented_objects
fitPlasqUnit.matrix	Non-documented_objects
fitQuantileNormFcn	Non-documented_objects
fitQuantileNormFcn,AffymetrixCelFile-method	fitQuantileNormFcn.AffymetrixCelFile
fitQuantileNormFcn.AffymetrixCelFile	fitQuantileNormFcn.AffymetrixCelFile
fixSearchPath.AromaAffymetrix	Non-documented_objects
FragmentEquivalentClassNormalization	FragmentEquivalentClassNormalization
FragmentEquivalentClassNormalization.process	process.FragmentEquivalentClassNormalization
FragmentLengthNormalization	FragmentLengthNormalization
FragmentLengthNormalization.process	process.FragmentLengthNormalization
fromCdf	Non-documented_objects
fromCdf,GenomeInformation-method	fromCdf.GenomeInformation
fromCdf,SnpInformation-method	fromCdf.SnpInformation
fromCdf.AffymetrixProbeTabFile	Non-documented_objects
fromCdf.GenomeInformation	fromCdf.GenomeInformation
fromCdf.SnpInformation	fromCdf.SnpInformation
fromChipType	Non-documented_objects
fromChipType.AffymetrixCsvGenomeInformation	Non-documented_objects
fromChipType.AffymetrixProbeTabFile	Non-documented_objects
fromChipType.AffymetrixTabularFile	Non-documented_objects
fromChipType.AffymetrixTsvFile	Non-documented_objects
fromChipType.AromaChipTypeAnnotationFile	Non-documented_objects
fromChipType.DChipGenomeInformation	Non-documented_objects
fromChipType.DChipSnpInformation	Non-documented_objects
fromChipType.GenomeInformation	Non-documented_objects
fromChipType.SnpInformation	Non-documented_objects
fromChipType.UflSnpInformation	Non-documented_objects
fromChipType.UgpGenomeInformation	Non-documented_objects
fromDataFile	Non-documented_objects
fromDataFile,ChipEffectFile-method	fromDataFile.ChipEffectFile
fromDataFile.ChipEffectFile	fromDataFile.ChipEffectFile
fromDataFile.FirmaFile	Non-documented_objects
fromDataFile.ResidualFile	Non-documented_objects
fromDataFile.WeightsFile	Non-documented_objects
fromDataSet	Non-documented_objects
fromDataSet.ChipEffectSet	Non-documented_objects
fromDataSet.FirmaSet	Non-documented_objects
fromDataSet.GenomeInformation	Non-documented_objects
fromDataSet.ResidualSet	Non-documented_objects
fromDataSet.SnpInformation	Non-documented_objects
fromDataSet.WeightsSet	Non-documented_objects
fromFile,AffymetrixCdfFile-method	fromFile.AffymetrixCdfFile
fromFile,AffymetrixCelFile-method	fromFile.AffymetrixCelFile
fromFile,AromaChipTypeAnnotationFile-method	fromFile.AromaChipTypeAnnotationFile
fromFile,CnagCfhFile-method	fromFile.CnagCfhFile
fromFile.AffymetrixCdfFile	fromFile.AffymetrixCdfFile
fromFile.AffymetrixCelFile	fromFile.AffymetrixCelFile
fromFile.AffymetrixCnChpFile	Non-documented_objects
fromFile.AromaChipTypeAnnotationFile	fromFile.AromaChipTypeAnnotationFile
fromFile.CnagCfhFile	fromFile.CnagCfhFile
fromFile.DChipCdfBinFile	Non-documented_objects
fromFile.DChipDcpFile	Non-documented_objects
fromName	Non-documented_objects
fromName.AffymetrixCelSet	Non-documented_objects
fromName.CnagCfhSet	Non-documented_objects
fromName.DChipDcpSet	Non-documented_objects
GcContentNormalization	GcContentNormalization
GcContentNormalization.process	process.GcContentNormalization
GcContentNormalization2	GcContentNormalization2
GcRmaBackgroundCorrection	GcRmaBackgroundCorrection
GcRmaBackgroundCorrection.process	process.GcRmaBackgroundCorrection
GenericReporter	GenericReporter
GenericReporter.getAlias	getAlias.GenericReporter
GenericReporter.getName	getName.GenericReporter
GenericReporter.getTags	getTags.GenericReporter
GenericReporter.process	process.GenericReporter
GenericReporter.setAlias	setAlias.GenericReporter
GenomeInformation	GenomeInformation
GenomeInformation.byChipType	byChipType.GenomeInformation
GenomeInformation.fromCdf	fromCdf.GenomeInformation
GenomeInformation.getChipType	getChipType.GenomeInformation
GenomeInformation.getData	getData.GenomeInformation
GenomeInformation.getPositions	getPositions.GenomeInformation
GenomeInformation.getUnitIndices	getUnitIndices.GenomeInformation
GenomeInformation.plotDensity	plotDensity.GenomeInformation
GenomeInformation.verify	verify.GenomeInformation
getACSFile	Non-documented_objects
getACSFile.AffymetrixCdfFile	Non-documented_objects
getAlias,GenericReporter-method	getAlias.GenericReporter
getAlias,Model-method	getAlias.Model
getAlias.ArrayExplorer	Non-documented_objects
getAlias.GenericReporter	getAlias.GenericReporter
getAlias.Model	getAlias.Model
getAlias.TransformReport	Non-documented_objects
getAlleleCellPairs	Non-documented_objects
getAlleleCellPairs,AffymetrixCdfFile-method	getAlleleCellPairs.AffymetrixCdfFile
getAlleleCellPairs.AffymetrixCdfFile	getAlleleCellPairs.AffymetrixCdfFile
getAlleleProbePairs	Non-documented_objects
getAlleleProbePairs,AffymetrixCdfFile-method	getAlleleProbePairs.AffymetrixCdfFile
getAlleleProbePairs.AffymetrixCdfFile	getAlleleProbePairs.AffymetrixCdfFile
getAlleleProbePairs2	Non-documented_objects
getAlleleProbePairs2.AffymetrixCdfFile	Non-documented_objects
getAlleleProbePairs3	Non-documented_objects
getAlleleProbePairs3,AffymetrixCdfFile-method	getAlleleProbePairs3.AffymetrixCdfFile
getAlleleProbePairs3.AffymetrixCdfFile	getAlleleProbePairs3.AffymetrixCdfFile
getAm	Non-documented_objects
getAM,ChipEffectFile-method	getAM.ChipEffectFile
getAM,ChipEffectSet-method	getAM.ChipEffectSet
getAm.AffymetrixCelFile	Non-documented_objects
getAM.ChipEffectFile	getAM.ChipEffectFile
getAM.ChipEffectSet	getAM.ChipEffectSet
getAromaCellMatchScoreFile	Non-documented_objects
getAromaCellMatchScoreFile.MatNormalization	Non-documented_objects
getAromaCellPositionFile	Non-documented_objects
getAromaCellPositionFile.MatSmoothing	Non-documented_objects
getAromaCellSequenceFile	Non-documented_objects
getAromaCellSequenceFile.AbstractProbeSequenceNormalization	Non-documented_objects
getAromaCellSequenceFile.AffymetrixCdfFile	Non-documented_objects
getAromaUfcFile	Non-documented_objects
getAromaUfcFile.FragmentEquivalentClassNormalization	Non-documented_objects
getAromaUflFile.UflSnpInformation	Non-documented_objects
getAromaUgpFile.UgpGenomeInformation	Non-documented_objects
getAromaUnitFracBCnBinarySet	Non-documented_objects
getAromaUnitFracBCnBinarySet.default	Non-documented_objects
getAromaUnitTotalCnBinarySet	Non-documented_objects
getAromaUnitTotalCnBinarySet.default	Non-documented_objects
getArrayNames	Non-documented_objects
getArrayNames.AffymetrixAptSummaryFile	Non-documented_objects
getArraysOfInput.ArrayExplorer	Non-documented_objects
getAsFullCelFile	Non-documented_objects
getAsFullCelFile.ChipEffectFile	Non-documented_objects
getAsFullCelSet	Non-documented_objects
getAsFullCelSet.ChipEffectSet	Non-documented_objects
getAsteriskTags.AdditiveCovariatesNormalization	Non-documented_objects
getAsteriskTags.AffineCnPlm	Non-documented_objects
getAsteriskTags.AffinePlm	Non-documented_objects
getAsteriskTags.AffineSnpPlm	Non-documented_objects
getAsteriskTags.AlleleSummation	Non-documented_objects
getAsteriskTags.AllelicCrosstalkCalibration	Non-documented_objects
getAsteriskTags.ArrayExplorer	Non-documented_objects
getAsteriskTags.AvgCnPlm	Non-documented_objects
getAsteriskTags.AvgPlm	Non-documented_objects
getAsteriskTags.AvgSnpPlm	Non-documented_objects
getAsteriskTags.BaseCountNormalization	Non-documented_objects
getAsteriskTags.BasePositionNormalization	Non-documented_objects
getAsteriskTags.CrlmmModel	Non-documented_objects
getAsteriskTags.ExonRmaPlm	Non-documented_objects
getAsteriskTags.FirmaModel	Non-documented_objects
getAsteriskTags.FragmentEquivalentClassNormalization	Non-documented_objects
getAsteriskTags.FragmentLengthNormalization	Non-documented_objects
getAsteriskTags.GenericReporter	Non-documented_objects
getAsteriskTags.HetLogAddCnPlm	Non-documented_objects
getAsteriskTags.HetLogAddPlm	Non-documented_objects
getAsteriskTags.HetLogAddSnpPlm	Non-documented_objects
getAsteriskTags.LimmaBackgroundCorrection	Non-documented_objects
getAsteriskTags.MatNormalization	Non-documented_objects
getAsteriskTags.MbeiCnPlm	Non-documented_objects
getAsteriskTags.MbeiPlm	Non-documented_objects
getAsteriskTags.MbeiSnpPlm	Non-documented_objects
getAsteriskTags.Model	Non-documented_objects
getAsteriskTags.NormExpBackgroundCorrection	Non-documented_objects
getAsteriskTags.ProbeLevelModel	Non-documented_objects
getAsteriskTags.ProbeLevelTransform3	Non-documented_objects
getAsteriskTags.QualityAssessmentModel	Non-documented_objects
getAsteriskTags.ReseqCrosstalkCalibration	Non-documented_objects
getAsteriskTags.RmaCnPlm	Non-documented_objects
getAsteriskTags.RmaPlm	Non-documented_objects
getAsteriskTags.RmaSnpPlm	Non-documented_objects
getAsteriskTags.ScaleNormalization	Non-documented_objects
getAsteriskTags.SmoothMultiarrayModel	Non-documented_objects
getAsteriskTags.SmoothRmaModel	Non-documented_objects
getAsteriskTags.SmoothSaModel	Non-documented_objects
getAsteriskTags.SnpChipEffectGroupMerge	Non-documented_objects
getAsteriskTags.UnitModel	Non-documented_objects
getAverage	Non-documented_objects
getAverage.AffymetrixCelSet	Non-documented_objects
getAverage.CnagCfhSet	Non-documented_objects
getAverageAsinh	Non-documented_objects
getAverageAsinh.AffymetrixCelSet	Non-documented_objects
getAverageAsinh.CnagCfhSet	Non-documented_objects
getAverageFile,AffymetrixCelSet-method	getAverageFile.AffymetrixCelSet
getAverageFile,CnagCfhSet-method	getAverageFile.CnagCfhSet
getAverageFile.AffymetrixCelSet	getAverageFile.AffymetrixCelSet
getAverageFile.ChipEffectSet	Non-documented_objects
getAverageFile.CnagCfhSet	getAverageFile.CnagCfhSet
getAverageFile.CnChipEffectSet	Non-documented_objects
getAverageFile.ExonChipEffectSet	Non-documented_objects
getAverageFile.ResidualSet	Non-documented_objects
getAverageFile.SnpChipEffectSet	Non-documented_objects
getAverageFile.WeightsSet	Non-documented_objects
getAverageLog	Non-documented_objects
getAverageLog.AffymetrixCelSet	Non-documented_objects
getAverageLog.CnagCfhSet	Non-documented_objects
getBandwidth	Non-documented_objects
getBandwidth.SmoothMultiarrayModel	Non-documented_objects
getBaseline	Non-documented_objects
getBaseline,ChipEffectSet-method	getBaseline.ChipEffectSet
getBaseline.ChipEffectSet	getBaseline.ChipEffectSet
getBaseline.CnChipEffectSet	Non-documented_objects
getBaseline.SnpChipEffectSet	Non-documented_objects
getBlockSizes	Non-documented_objects
getBlockSizes.SpatialRowColumnNormalization	Non-documented_objects
getCalculateResidualsFunction	Non-documented_objects
getCalculateResidualsFunction.AvgPlm	Non-documented_objects
getCalculateResidualsFunction.ProbeLevelModel	Non-documented_objects
getCalculateResidualsFunction.RmaPlm	Non-documented_objects
getCalls	Non-documented_objects
getCalls.DChipDcpFile	Non-documented_objects
getCallSet	Non-documented_objects
getCallSet.CrlmmModel	Non-documented_objects
getCdf	Non-documented_objects
getCdf,AffymetrixCelFile-method	getCdf.AffymetrixCelFile
getCdf,AffymetrixCelSet-method	getCdf.AffymetrixCelSet
getCdf,CnagCfhFile-method	getCdf.CnagCfhFile
getCdf,CnagCfhSet-method	getCdf.CnagCfhSet
getCdf,Model-method	getCdf.Model
getCdf.AdditiveCovariatesNormalization	Non-documented_objects
getCdf.AffymetrixCelFile	getCdf.AffymetrixCelFile
getCdf.AffymetrixCelSet	getCdf.AffymetrixCelSet
getCdf.AffymetrixCnChpFile	Non-documented_objects
getCdf.AffymetrixCnChpSet	Non-documented_objects
getCdf.AffymetrixProbeTabFile	Non-documented_objects
getCdf.AffymetrixTsvFile	Non-documented_objects
getCdf.AromaUnitTabularBinaryFile	Non-documented_objects
getCdf.ChipEffectGroupMerge	Non-documented_objects
getCdf.CnagCfhFile	getCdf.CnagCfhFile
getCdf.CnagCfhSet	getCdf.CnagCfhSet
getCdf.FirmaModel	Non-documented_objects
getCdf.FragmentEquivalentClassNormalization	Non-documented_objects
getCdf.FragmentLengthNormalization	Non-documented_objects
getCdf.GcContentNormalization	Non-documented_objects
getCdf.Model	getCdf.Model
getCdf.QualityAssessmentModel	Non-documented_objects
getCdf.TransformReport	Non-documented_objects
getCdfBin	Non-documented_objects
getCdfBin.DChipDcpSet	Non-documented_objects
getCellDim	Non-documented_objects
getCellDim.DChipCdfBinFile	Non-documented_objects
getCellIndices	Non-documented_objects
getCellIndices,AffymetrixCdfFile-method	getCellIndices.AffymetrixCdfFile
getCellIndices,UnitModel-method	getCellIndices.UnitModel
getCellIndices.AffymetrixCdfFile	getCellIndices.AffymetrixCdfFile
getCellIndices.ChipEffectFile	Non-documented_objects
getCellIndices.ChipEffectSet	Non-documented_objects
getCellIndices.CnChipEffectFile	Non-documented_objects
getCellIndices.CnPlm	Non-documented_objects
getCellIndices.CnProbeAffinityFile	Non-documented_objects
getCellIndices.ExonChipEffectFile	Non-documented_objects
getCellIndices.ExonProbeAffinityFile	Non-documented_objects
getCellIndices.ExonRmaPlm	Non-documented_objects
getCellIndices.FirmaFile	Non-documented_objects
getCellIndices.FirmaSet	Non-documented_objects
getCellIndices.ProbeAffinityFile	Non-documented_objects
getCellIndices.ResidualFile	Non-documented_objects
getCellIndices.ResidualSet	Non-documented_objects
getCellIndices.SnpChipEffectFile	Non-documented_objects
getCellIndices.SnpPlm	Non-documented_objects
getCellIndices.SnpProbeAffinityFile	Non-documented_objects
getCellIndices.UnitModel	getCellIndices.UnitModel
getCellIndices.WeightsFile	Non-documented_objects
getCellIndices.WeightsSet	Non-documented_objects
getCellMap	Non-documented_objects
getCellMap,ChipEffectFile-method	getUnitGroupCellMap.ChipEffectFile
getCellMap.ChipEffectFile	getUnitGroupCellMap.ChipEffectFile
getCellMap.FirmaFile	Non-documented_objects
getCellMap.ResidualFile	Non-documented_objects
getCellMap.WeightsFile	Non-documented_objects
getCellMapForMainCdf	Non-documented_objects
getCellMapForMainCdf.ChipEffectFile	Non-documented_objects
getCellQuartets	Non-documented_objects
getCellQuartets.AffymetrixCdfFile	Non-documented_objects
getCellsTo	Non-documented_objects
getCellsTo.ProbeLevelTransform3	Non-documented_objects
getCellsToFit	Non-documented_objects
getCellsToFit.ProbeLevelTransform3	Non-documented_objects
getCellsToInternal	Non-documented_objects
getCellsToInternal.ProbeLevelTransform3	Non-documented_objects
getCellsToUpdate	Non-documented_objects
getCellsToUpdate.ProbeLevelTransform3	Non-documented_objects
getChipEffectFileClass	Non-documented_objects
getChipEffectFileClass.ChipEffectSet	Non-documented_objects
getChipEffectFileClass.CnChipEffectSet	Non-documented_objects
getChipEffectFileClass.ExonChipEffectSet	Non-documented_objects
getChipEffectFileClass.SnpChipEffectSet	Non-documented_objects
getChipEffects	Non-documented_objects
getChipEffects,ProbeLevelModel-method	getChipEffectSet.ProbeLevelModel
getChipEffects.ExonRmaPlm	Non-documented_objects
getChipEffects.ProbeLevelModel	getChipEffectSet.ProbeLevelModel
getChipEffects.QualityAssessmentModel	Non-documented_objects
getChipEffectSet	Non-documented_objects
getChipEffectSet,AlleleSummation-method	getChipEffectSet.AlleleSummation
getChipEffectSet,ProbeLevelModel-method	getChipEffectSet.ProbeLevelModel
getChipEffectSet.AlleleSummation	getChipEffectSet.AlleleSummation
getChipEffectSet.CnPlm	Non-documented_objects
getChipEffectSet.ExonRmaPlm	Non-documented_objects
getChipEffectSet.ProbeLevelModel	getChipEffectSet.ProbeLevelModel
getChipEffectSet.QualityAssessmentModel	Non-documented_objects
getChipEffectSet.SnpPlm	Non-documented_objects
getChipEffectSetClass	Non-documented_objects
getChipEffectSetClass.AlleleSummation	Non-documented_objects
getChipEffectSetClass.CnPlm	Non-documented_objects
getChipEffectSetClass.ExonRmaPlm	Non-documented_objects
getChipEffectSetClass.ProbeLevelModel	Non-documented_objects
getChipEffectSetClass.SnpPlm	Non-documented_objects
getChipType,AffymetrixCelFile-method	getChipType.AffymetrixCelFile
getChipType,AffymetrixCelSet-method	getChipType.AffymetrixCelSet
getChipType,CnagCfhFile-method	getChipType.CnagCfhFile
getChipType,GenomeInformation-method	getChipType.GenomeInformation
getChipType,SnpInformation-method	getChipType.SnpInformation
getChipType.AffymetrixAptSummaryFile	Non-documented_objects
getChipType.AffymetrixCdfFile	Non-documented_objects
getChipType.AffymetrixCelFile	getChipType.AffymetrixCelFile
getChipType.AffymetrixCelSet	getChipType.AffymetrixCelSet
getChipType.AffymetrixCelSetReporter	Non-documented_objects
getChipType.AffymetrixCnChpFile	Non-documented_objects
getChipType.AffymetrixProbeTabFile	Non-documented_objects
getChipType.AffymetrixTsvFile	Non-documented_objects
getChipType.AromaChipTypeAnnotationFile	Non-documented_objects
getChipType.CnagCfhFile	getChipType.CnagCfhFile
getChipType.CrlmmModel	Non-documented_objects
getChipType.DChipCdfBinFile	Non-documented_objects
getChipType.DChipDcpSet	Non-documented_objects
getChipType.GenomeInformation	getChipType.GenomeInformation
getChipType.SnpInformation	getChipType.SnpInformation
getChipType.UflSnpInformation	Non-documented_objects
getChipType.UgpGenomeInformation	Non-documented_objects
getChromosomes.GenomeInformation	Non-documented_objects
getChromosomes.UgpGenomeInformation	Non-documented_objects
getChromosomeStats	Non-documented_objects
getChromosomeStats.GenomeInformation	Non-documented_objects
getCnNames	Non-documented_objects
getCnNames,AffymetrixCdfFile-method	getCnNames.AffymetrixCdfFile
getCnNames.AffymetrixCdfFile	getCnNames.AffymetrixCdfFile
getColorMaps	Non-documented_objects
getColorMaps.ArrayExplorer	Non-documented_objects
getColorMaps.SpatialReporter	Non-documented_objects
getColumnNames.AffymetrixProbeTabFile	Non-documented_objects
getColumnNames.AromaCellMatchScoreFile	Non-documented_objects
getColumnNames.AromaUfcFile	Non-documented_objects
getColumnNames.AromaUnitGcContentFile	Non-documented_objects
getCombineAlleles	Non-documented_objects
getCombineAlleles.CnChipEffectSet	Non-documented_objects
getCombineAlleles.CnPlm	Non-documented_objects
getConfidenceScoreSet	Non-documented_objects
getConfidenceScoreSet.CrlmmModel	Non-documented_objects
getCovariates	Non-documented_objects
getCovariates.AdditiveCovariatesNormalization	Non-documented_objects
getCovariates.GcContentNormalization2	Non-documented_objects
getCrlmmParametersSet	Non-documented_objects
getCrlmmParametersSet.CrlmmModel	Non-documented_objects
getCrlmmPriors	Non-documented_objects
getCrlmmPriors.CrlmmModel	Non-documented_objects
getCrlmmSNPs	Non-documented_objects
getCrlmmSNPs.CrlmmModel	Non-documented_objects
getCrlmmSNPsOnChrX	Non-documented_objects
getCrlmmSNPsOnChrX.CrlmmModel	Non-documented_objects
getCrlmmSplineParameters	Non-documented_objects
getCrlmmSplineParameters.CrlmmModel	Non-documented_objects
getData	Non-documented_objects
getData,AffymetrixCelFile-method	readRawData.AffymetrixCelFile
getData,GenomeInformation-method	getData.GenomeInformation
getData,SnpInformation-method	getData.SnpInformation
getData.AffymetrixCelFile	readRawData.AffymetrixCelFile
getData.AffymetrixCelSet	Non-documented_objects
getData.AffymetrixCnChpFile	Non-documented_objects
getData.AffymetrixProbeTabFile	Non-documented_objects
getData.AffymetrixTsvFile	Non-documented_objects
getData.CnagCfhSet	Non-documented_objects
getData.GenomeInformation	getData.GenomeInformation
getData.SnpInformation	getData.SnpInformation
getData.UflSnpInformation	Non-documented_objects
getData.UgpGenomeInformation	Non-documented_objects
getDataColumns	Non-documented_objects
getDataColumns.GenomeInformation	Non-documented_objects
getDataColumns.UflSnpInformation	Non-documented_objects
getDataColumns.UgpGenomeInformation	Non-documented_objects
getDataFlat	Non-documented_objects
getDataFlat.ChipEffectFile	Non-documented_objects
getDataFlat.FirmaFile	Non-documented_objects
getDataFlat.ResidualFile	Non-documented_objects
getDataFlat.WeightsFile	Non-documented_objects
getDataPairs	Non-documented_objects
getDataPairs.AllelicCrosstalkCalibration	Non-documented_objects
getDataSet	Non-documented_objects
getDataSet,AffymetrixCelSetReporter-method	getDataSet.AffymetrixCelSetReporter
getDataSet,ArrayExplorer-method	getDataSet.ArrayExplorer
getDataSet,Model-method	getDataSet.Model
getDataSet.AffymetrixCelSetReporter	getDataSet.AffymetrixCelSetReporter
getDataSet.ArrayExplorer	getDataSet.ArrayExplorer
getDataSet.FirmaModel	Non-documented_objects
getDataSet.Model	getDataSet.Model
getDataSet.QualityAssessmentModel	Non-documented_objects
getDefaultExtension.AffymetrixCdfFile	Non-documented_objects
getDefaultExtension.AffymetrixCsvFile	Non-documented_objects
getDefaultExtension.AffymetrixCsvGenomeInformation	Non-documented_objects
getDefaultExtension.AffymetrixNetAffxCsvFile	Non-documented_objects
getDefaultExtension.AffymetrixTsvFile	Non-documented_objects
getDefaultExtension.AromaCellMatchScoreFile	Non-documented_objects
getDefaultExtension.AromaChipTypeAnnotationFile	Non-documented_objects
getDefaultFullName.AffymetrixFileSet	Non-documented_objects
getDefaultFullName.CnagCfhSet	Non-documented_objects
getDefaultSettings	Non-documented_objects
getDefaultSettings.AromaAffymetrix	Non-documented_objects
getDefaultSettings.Package	Non-documented_objects
getDesignMatrix	Non-documented_objects
getDesignMatrix.BaseCountNormalization	Non-documented_objects
getDesignMatrix.BasePositionNormalization	Non-documented_objects
getDesignMatrix.LinearModelProbeSequenceNormalization	Non-documented_objects
getDesignMatrix.MatNormalization	Non-documented_objects
getDimension	Non-documented_objects
getDimension.AffymetrixCdfFile	Non-documented_objects
getExclCells	Non-documented_objects
getExclCells.DChipQuantileNormalization	Non-documented_objects
getExclCells.QuantileNormalization	Non-documented_objects
getExcludes	Non-documented_objects
getExcludes.DChipDcpFile	Non-documented_objects
getExclusiveUnitSubsets	Non-documented_objects
getExclusiveUnitSubsets.FragmentEquivalentClassNormalization	Non-documented_objects
getExpandedCellMap	Non-documented_objects
getExpandedCellMap.ChipEffectFile	Non-documented_objects
getExpandedCellMap.CnChipEffectFile	Non-documented_objects
getExpandedCellMap.SnpChipEffectFile	Non-documented_objects
getExpectedOutputFiles.MatSmoothing	Non-documented_objects
getExpectedOutputFullnames.MatSmoothing	Non-documented_objects
getExtensionPattern.AffymetrixCdfFile	Non-documented_objects
getExtensionPattern.AffymetrixCelFile	Non-documented_objects
getExtensionPattern.AffymetrixCnChpFile	Non-documented_objects
getExtensionPattern.AffymetrixCsvFile	Non-documented_objects
getExtensionPattern.AffymetrixTsvFile	Non-documented_objects
getExtensionPattern.AromaCellMatchScoreFile	Non-documented_objects
getExtensionPattern.AromaUfcFile	Non-documented_objects
getExtensionPattern.AromaUnitGcContentFile	Non-documented_objects
getExtensionPattern.CnagCfhFile	Non-documented_objects
getExtensionPattern.DChipDcpFile	Non-documented_objects
getField	Non-documented_objects
getField.AffymetrixTsvFile	Non-documented_objects
getFields.SnpInformation	Non-documented_objects
getFields.UflSnpInformation	Non-documented_objects
getFileClass.FirmaSet	Non-documented_objects
getFileFormat	Non-documented_objects
getFileFormat.AffymetrixCdfFile	Non-documented_objects
getFileFormat.AffymetrixCelFile	Non-documented_objects
getFileFormat.AffymetrixCnChpFile	Non-documented_objects
getFileFormat.DChipCdfBinFile	Non-documented_objects
getFileFormat.DChipDcpFile	Non-documented_objects
getFilenameExtension.AromaCellMatchScoreFile	Non-documented_objects
getFilenameExtension.AromaUfcFile	Non-documented_objects
getFilenameExtension.AromaUnitGcContentFile	Non-documented_objects
getFileSet	Non-documented_objects
getFileSet.AffymetrixFileSetReporter	Non-documented_objects
getFileSetClass	Non-documented_objects
getFileSetClass.FirmaModel	Non-documented_objects
getFilteredFragmentLengths	Non-documented_objects
getFilteredFragmentLengths.FragmentLengthNormalization	Non-documented_objects
getFirmaScores	Non-documented_objects
getFirmaScores,FirmaModel-method	getFirmaSet.FirmaModel
getFirmaScores.FirmaModel	getFirmaSet.FirmaModel
getFirmaSet	Non-documented_objects
getFirmaSet,FirmaModel-method	getFirmaSet.FirmaModel
getFirmaSet.FirmaModel	getFirmaSet.FirmaModel
getFirstCellIndices	Non-documented_objects
getFirstCellIndices.AffymetrixCdfFile	Non-documented_objects
getFirstCellPerUnitIndices	Non-documented_objects
getFirstCellPerUnitIndices.ExonChipEffectSet	Non-documented_objects
getFit	Non-documented_objects
getFit.BasePositionNormalization	Non-documented_objects
getFitFunction.MultiArrayUnitModel	Non-documented_objects
getFitSingleCellUnitFunction	Non-documented_objects
getFitSingleCellUnitFunction.UnitModel	Non-documented_objects
getFitUnitFunction	Non-documented_objects
getFitUnitFunction.CnPlm	Non-documented_objects
getFitUnitFunction.FirmaModel	Non-documented_objects
getFitUnitFunction.MultiArrayUnitModel	Non-documented_objects
getFitUnitFunction.SingleArrayUnitModel	Non-documented_objects
getFitUnitFunction.UnitModel	Non-documented_objects
getFitUnitGroupFunction	Non-documented_objects
getFitUnitGroupFunction,AffinePlm-method	getFitUnitGroupFunction.AffinePlm
getFitUnitGroupFunction,AvgPlm-method	getFitUnitGroupFunction.AvgPlm
getFitUnitGroupFunction,ExonRmaPlm-method	getFitUnitGroupFunction.ExonRmaPlm
getFitUnitGroupFunction,FirmaModel-method	getFitUnitGroupFunction.FirmaModel
getFitUnitGroupFunction,HetLogAddPlm-method	getFitUnitGroupFunction.HetLogAddPlm
getFitUnitGroupFunction,MbeiPlm-method	getFitUnitGroupFunction.MbeiPlm
getFitUnitGroupFunction,MultiArrayUnitModel-method	getFitUnitGroupFunction.MultiArrayUnitModel
getFitUnitGroupFunction,RmaPlm-method	getFitUnitGroupFunction.RmaPlm
getFitUnitGroupFunction,SingleArrayUnitModel-method	getFitUnitGroupFunction.SingleArrayUnitModel
getFitUnitGroupFunction.AffinePlm	getFitUnitGroupFunction.AffinePlm
getFitUnitGroupFunction.AvgPlm	getFitUnitGroupFunction.AvgPlm
getFitUnitGroupFunction.ExonRmaPlm	getFitUnitGroupFunction.ExonRmaPlm
getFitUnitGroupFunction.FirmaModel	getFitUnitGroupFunction.FirmaModel
getFitUnitGroupFunction.HetLogAddPlm	getFitUnitGroupFunction.HetLogAddPlm
getFitUnitGroupFunction.MbeiPlm	getFitUnitGroupFunction.MbeiPlm
getFitUnitGroupFunction.MultiArrayUnitModel	getFitUnitGroupFunction.MultiArrayUnitModel
getFitUnitGroupFunction.RmaPlm	getFitUnitGroupFunction.RmaPlm
getFitUnitGroupFunction.SingleArrayUnitModel	getFitUnitGroupFunction.SingleArrayUnitModel
getFitUnitGroupFunction.SmoothMultiarrayModel	Non-documented_objects
getFitUnitGroupFunction.SmoothRmaModel	Non-documented_objects
getFitUnitGroupFunction.SmoothSaModel	Non-documented_objects
getFragmentLengths	Non-documented_objects
getFragmentLengths.AffymetrixTsvFile	Non-documented_objects
getFragmentLengths.SnpInformation	Non-documented_objects
getFragmentLengths.UflSnpInformation	Non-documented_objects
getFragmentStarts	Non-documented_objects
getFragmentStarts.SnpInformation	Non-documented_objects
getFragmentStarts.UflSnpInformation	Non-documented_objects
getFragmentStops	Non-documented_objects
getFragmentStops.SnpInformation	Non-documented_objects
getFragmentStops.UflSnpInformation	Non-documented_objects
getFullName,Model-method	getFullName.Model
getFullName,TransformReport-method	getFullName.TransformReport
getFullName.GenericReporter	Non-documented_objects
getFullName.Model	getFullName.Model
getFullName.QualityAssessmentModel	Non-documented_objects
getFullName.TransformReport	getFullName.TransformReport
getFullNames.ChipEffectSetTuple	Non-documented_objects
getGc	Non-documented_objects
getGc.AffymetrixTsvFile	Non-documented_objects
getGcContent	Non-documented_objects
getGcContent.GcContentNormalization	Non-documented_objects
getGenomeBuild	Non-documented_objects
getGenomeBuild.AffymetrixNetAffxCsvFile	Non-documented_objects
getGenomeInformation	Non-documented_objects
getGenomeInformation,AffymetrixCdfFile-method	getGenomeInformation.AffymetrixCdfFile
getGenomeInformation.AffymetrixCdfFile	getGenomeInformation.AffymetrixCdfFile
getGroupDirections	Non-documented_objects
getGroupDirections.AffymetrixCdfFile	Non-documented_objects
getHeader,AffymetrixCdfFile-method	getHeader.AffymetrixCdfFile
getHeader,AffymetrixCelFile-method	getHeader.AffymetrixCelFile
getHeader,AromaChipTypeAnnotationFile-method	getHeader.AromaChipTypeAnnotationFile
getHeader,CnagCfhFile-method	getHeader.CnagCfhFile
getHeader.AffymetrixCdfFile	getHeader.AffymetrixCdfFile
getHeader.AffymetrixCelFile	getHeader.AffymetrixCelFile
getHeader.AffymetrixCnChpFile	Non-documented_objects
getHeader.AromaChipTypeAnnotationFile	getHeader.AromaChipTypeAnnotationFile
getHeader.CnagCfhFile	getHeader.CnagCfhFile
getHeader.DChipCdfBinFile	Non-documented_objects
getHeader.DChipDcpFile	Non-documented_objects
getHeaderAttributes	Non-documented_objects
getHeaderAttributes.AffymetrixNetAffxCsvFile	Non-documented_objects
getHeaderLength	Non-documented_objects
getHeaderLength.CnagCfhFile	Non-documented_objects
getHeaderV3	Non-documented_objects
getHeaderV3.AffymetrixCelFile	Non-documented_objects
getIdentifier	Non-documented_objects
getIdentifier.AffymetrixCelFile	Non-documented_objects
getIdentifier.AffymetrixCelSet	Non-documented_objects
getIdentifier.AffymetrixFileSet	Non-documented_objects
getIdentifier.CnagCfhFile	Non-documented_objects
getIdentifier.CnagCfhSet	Non-documented_objects
getImage,AffymetrixCelFile-method	getImage.AffymetrixCelFile
getImage.AffymetrixCdfFile	Non-documented_objects
getImage.AffymetrixCelFile	getImage.AffymetrixCelFile
getImage.AromaUnitTabularBinaryFile	Non-documented_objects
getImage.ResidualFile	Non-documented_objects
getImage.WeightsFile	Non-documented_objects
getIndexToRowMap	Non-documented_objects
getIndexToRowMap.AffymetrixProbeTabFile	Non-documented_objects
getInputDataSet,TransformReport-method	getInputDataSet.TransformReport
getInputDataSet.TransformReport	getInputDataSet.TransformReport
getInputName	Non-documented_objects
getInputName.AffymetrixFileSetReporter	Non-documented_objects
getInputName.GenericReporter	Non-documented_objects
getInputTags	Non-documented_objects
getInputTags.AffymetrixFileSetReporter	Non-documented_objects
getInputTags.GenericReporter	Non-documented_objects
getIntensities	Non-documented_objects
getIntensities,AffymetrixCelSet-method	getIntensities.AffymetrixCelSet
getIntensities.AffymetrixCelSet	getIntensities.AffymetrixCelSet
getLabel.Model	Non-documented_objects
getListOfCdfs	Non-documented_objects
getListOfCdfs.AffymetrixCelSetTuple	Non-documented_objects
getListOfGenomeInformations	Non-documented_objects
getListOfGenomeInformations.ChromosomalModel	Non-documented_objects
getListOfPriors	Non-documented_objects
getListOfPriors.MultiArrayUnitModel	Non-documented_objects
getListOfReporters	Non-documented_objects
getListOfReporters.ArrayExplorer	Non-documented_objects
getListOfUnitNamesFiles.AffymetrixCelSetTuple	Non-documented_objects
getListOfUnitNamesFiles.ArrayExplorer	Non-documented_objects
getListOfUnitTypesFiles.AffymetrixCelSetTuple	Non-documented_objects
getListOfUnitTypesFiles.ArrayExplorer	Non-documented_objects
getMainCdf	Non-documented_objects
getMainCdf.AffymetrixCdfFile	Non-documented_objects
getMainPath.GenericReporter	Non-documented_objects
getMatrixChipEffectFiles	Non-documented_objects
getMatrixChipEffectFiles.CopyNumberChromosomalModel	Non-documented_objects
getMergeFunction	Non-documented_objects
getMergeFunction.ChipEffectGroupMerge	Non-documented_objects
getMergeFunction.SnpChipEffectGroupMerge	Non-documented_objects
getMergeGroups	Non-documented_objects
getMergeGroups.ExonChipEffectSet	Non-documented_objects
getMergeStrands	Non-documented_objects
getMergeStrands.SnpChipEffectSet	Non-documented_objects
getMergeStrands.SnpPlm	Non-documented_objects
getMonoCell	Non-documented_objects
getMonoCell.AffymetrixCdfFile	Non-documented_objects
getMonocellCdf	Non-documented_objects
getMonocellCdf.AffymetrixCdfFile	Non-documented_objects
getName,GenericReporter-method	getName.GenericReporter
getName,Model-method	getName.Model
getName,TransformReport-method	getName.TransformReport
getName.AffymetrixPlatform	Non-documented_objects
getName.FirmaModel	Non-documented_objects
getName.GenericReporter	getName.GenericReporter
getName.Model	getName.Model
getName.QualityAssessmentModel	Non-documented_objects
getName.TransformReport	getName.TransformReport
getNameOfInput.ArrayExplorer	Non-documented_objects
getNetAffxBuild	Non-documented_objects
getNetAffxBuild.AffymetrixNetAffxCsvFile	Non-documented_objects
getNetAffxDate	Non-documented_objects
getNetAffxDate.AffymetrixNetAffxCsvFile	Non-documented_objects
getNormalEquations	Non-documented_objects
getNormalEquations.LinearModelProbeSequenceNormalization	Non-documented_objects
getNormalizedIntensities	Non-documented_objects
getNormalizedIntensities.DChipDcpFile	Non-documented_objects
getNormalizeSignalsOne	Non-documented_objects
getNormalizeSignalsOne.ScaleNormalization3	Non-documented_objects
getNormalizeSignalsOne.UnitTypeScaleNormalization	Non-documented_objects
getNumberOfFilesAveraged.CnChipEffectFile	Non-documented_objects
getOption	Non-documented_objects
getOrderedFragmentPairMap	Non-documented_objects
getOrderedFragmentPairMap.AromaUfcFile	Non-documented_objects
getOrderedFragmentPairs	Non-documented_objects
getOrderedFragmentPairs.AromaUfcFile	Non-documented_objects
getOutputDataSet,Transform-method	getOutputDataSet.Transform
getOutputDataSet,TransformReport-method	getOutputDataSet.TransformReport
getOutputDataSet.Transform	getOutputDataSet.Transform
getOutputDataSet.TransformReport	getOutputDataSet.TransformReport
getOutputDataSet00	Non-documented_objects
getOutputDataSet00.AdditiveCovariatesNormalization	Non-documented_objects
getOutputDataSet00.FragmentEquivalentClassNormalization	Non-documented_objects
getOutputDataSet00.FragmentLengthNormalization	Non-documented_objects
getOutputDataSet00.GcContentNormalization	Non-documented_objects
getOutputDataSetOLD20090509	Non-documented_objects
getOutputDataSetOLD20090509.Transform	Non-documented_objects
getOutputFiles.Transform	Non-documented_objects
getOutputIdentifier	Non-documented_objects
getOutputIdentifier.QuantileNormalization	Non-documented_objects
getOutputTuple	Non-documented_objects
getOutputTuple.SmoothMultiarrayModel	Non-documented_objects
getPackageName	Non-documented_objects
getParameter.AffymetrixAptSummaryFile	Non-documented_objects
getParameters.AbstractProbeSequenceNormalization	Non-documented_objects
getParameters.AdditiveCovariatesNormalization	Non-documented_objects
getParameters.AllelicCrosstalkCalibration	Non-documented_objects
getParameters.BackgroundCorrection	Non-documented_objects
getParameters.BaseCountNormalization	Non-documented_objects
getParameters.BasePositionNormalization	Non-documented_objects
getParameters.ChipEffectFile	Non-documented_objects
getParameters.ChipEffectGroupMerge	Non-documented_objects
getParameters.ChipEffectSet	Non-documented_objects
getParameters.CnChipEffectFile	Non-documented_objects
getParameters.DChipQuantileNormalization	Non-documented_objects
getParameters.ExonChipEffectFile	Non-documented_objects
getParameters.FragmentEquivalentClassNormalization	Non-documented_objects
getParameters.FragmentLengthNormalization	Non-documented_objects
getParameters.GcContentNormalization	Non-documented_objects
getParameters.GcRmaBackgroundCorrection	Non-documented_objects
getParameters.LimmaBackgroundCorrection	Non-documented_objects
getParameters.MatNormalization	Non-documented_objects
getParameters.MatSmoothing	Non-documented_objects
getParameters.Model	Non-documented_objects
getParameters.NormExpBackgroundCorrection	Non-documented_objects
getParameters.OpticalBackgroundCorrection	Non-documented_objects
getParameters.ParameterCelFile	Non-documented_objects
getParameters.ProbeAffinityFile	Non-documented_objects
getParameters.ProbeLevelTransform3	Non-documented_objects
getParameters.QuantileNormalization	Non-documented_objects
getParameters.ReseqCrosstalkCalibration	Non-documented_objects
getParameters.ResidualFile	Non-documented_objects
getParameters.ResidualSet	Non-documented_objects
getParameters.RmaBackgroundCorrection	Non-documented_objects
getParameters.ScaleNormalization	Non-documented_objects
getParameters.ScaleNormalization3	Non-documented_objects
getParameters.SnpChipEffectFile	Non-documented_objects
getParameters.SnpChipEffectGroupMerge	Non-documented_objects
getParameters.SpatialRowColumnNormalization	Non-documented_objects
getParameters.UnitTypeScaleNormalization	Non-documented_objects
getParameters.WeightsFile	Non-documented_objects
getParameters.WeightsSet	Non-documented_objects
getParametersAsString.ChipEffectFile	Non-documented_objects
getParametersAsString.ChipEffectSet	Non-documented_objects
getParametersAsString.Model	Non-documented_objects
getParametersAsString.ProbeAffinityFile	Non-documented_objects
getParametersAsString.ResidualFile	Non-documented_objects
getParametersAsString.ResidualSet	Non-documented_objects
getParametersAsString.WeightsFile	Non-documented_objects
getParametersAsString.WeightsSet	Non-documented_objects
getParameterSet	Non-documented_objects
getParameterSet.AvgPlm	Non-documented_objects
getParameterSet.CnPlm	Non-documented_objects
getParameterSet.CrlmmModel	Non-documented_objects
getParameterSet.ExonRmaPlm	Non-documented_objects
getParameterSet.Model	Non-documented_objects
getParameterSet.RmaPlm	Non-documented_objects
getParameterSet.SnpPlm	Non-documented_objects
getParameterSet.UnitModel	Non-documented_objects
getPath,Model-method	getPath.Model
getPath,TransformReport-method	getPath.TransformReport
getPath.AffymetrixCelSetReporter	Non-documented_objects
getPath.GenericReporter	Non-documented_objects
getPath.Model	getPath.Model
getPath.QualityAssessmentModel	Non-documented_objects
getPath.TransformReport	getPath.TransformReport
getPcuTheta	Non-documented_objects
getPcuTheta.ChromosomalModel	Non-documented_objects
getPlasqTypes	Non-documented_objects
getPlatform.AffymetrixCdfFile	Non-documented_objects
getPlatform.AffymetrixCelFile	Non-documented_objects
getPlatform.AffymetrixCelSet	Non-documented_objects
getPlatform.AromaChipTypeAnnotationFile	Non-documented_objects
getPlatform.DChipCdfBinFile	Non-documented_objects
getPlatformDesignDB	Non-documented_objects
getPlatformDesignDB.CrlmmModel	Non-documented_objects
getPlm	Non-documented_objects
getPlm.FirmaModel	Non-documented_objects
getPlm.QualityAssessmentModel	Non-documented_objects
getPosition.AffymetrixTsvFile	Non-documented_objects
getPositionChipTypeUnit	Non-documented_objects
getPositionChipTypeUnit.ChromosomalModel	Non-documented_objects
getPositionChipTypeUnit.CopyNumberSegmentationModel	Non-documented_objects
getPositions,GenomeInformation-method	getPositions.GenomeInformation
getPositions.GenomeInformation	getPositions.GenomeInformation
getProbeAffinities	Non-documented_objects
getProbeAffinities,ProbeLevelModel-method	getProbeAffinityFile.ProbeLevelModel
getProbeAffinities.ExonRmaPlm	Non-documented_objects
getProbeAffinities.ProbeLevelModel	getProbeAffinityFile.ProbeLevelModel
getProbeAffinityFile	Non-documented_objects
getProbeAffinityFile,ProbeLevelModel-method	getProbeAffinityFile.ProbeLevelModel
getProbeAffinityFile.AffinePlm	Non-documented_objects
getProbeAffinityFile.AvgPlm	Non-documented_objects
getProbeAffinityFile.CnPlm	Non-documented_objects
getProbeAffinityFile.ExonRmaPlm	Non-documented_objects
getProbeAffinityFile.MbeiPlm	Non-documented_objects
getProbeAffinityFile.ProbeLevelModel	getProbeAffinityFile.ProbeLevelModel
getProbeAffinityFile.RmaPlm	Non-documented_objects
getProbeAffinityFile.SnpPlm	Non-documented_objects
getProbeSequenceData	Non-documented_objects
getProbeSequenceData.AffymetrixCdfFile	Non-documented_objects
getProbesetIds	Non-documented_objects
getProbesetIds.AffymetrixAptSummaryFile	Non-documented_objects
getQuantificationScale	Non-documented_objects
getQuantificationScale.AffymetrixAptSummaryFile	Non-documented_objects
getRawIntensities	Non-documented_objects
getRawIntensities.DChipDcpFile	Non-documented_objects
getReadArguments.AffymetrixAptSummaryFile	Non-documented_objects
getRectangle	Non-documented_objects
getRectangle.AffymetrixCelFile	Non-documented_objects
getReference	Non-documented_objects
getReference.SpatialReporter	Non-documented_objects
getRegions.profileCGH	Non-documented_objects
getReportSet	Non-documented_objects
getReportSet.GenericReporter	Non-documented_objects
getReportSet.SpatialReporter	Non-documented_objects
getResidualFileClass	Non-documented_objects
getResidualFileClass.ResidualSet	Non-documented_objects
getResiduals	Non-documented_objects
getResiduals,QualityAssessmentModel-method	getResiduals.QualityAssessmentModel
getResiduals.QualityAssessmentModel	getResiduals.QualityAssessmentModel
getResidualSet	Non-documented_objects
getResidualSet.ProbeLevelModel	Non-documented_objects
getResidualSetClass	Non-documented_objects
getResidualSetClass.ProbeLevelModel	Non-documented_objects
getRestructor	Non-documented_objects
getRestructor.AffymetrixCdfFile	Non-documented_objects
getRlmFitFunctions	Non-documented_objects
getRlmFitFunctions.RmaPlm	Non-documented_objects
getRootPath,Model-method	getRootPath.Model
getRootPath.AlleleSummation	Non-documented_objects
getRootPath.ChipEffectTransform	Non-documented_objects
getRootPath.CrlmmModel	Non-documented_objects
getRootPath.FirmaModel	Non-documented_objects
getRootPath.GenericReporter	Non-documented_objects
getRootPath.Model	getRootPath.Model
getRootPath.ProbeLevelModel	Non-documented_objects
getRootPath.ProbeLevelTransform	Non-documented_objects
getRootPath.QualityAssessmentModel	Non-documented_objects
getRootPath.SmoothMultiarrayModel	Non-documented_objects
getRootPath.SmoothRmaModel	Non-documented_objects
getRootPath.TransformReport	Non-documented_objects
getSetsOfProbes	Non-documented_objects
getSetsOfProbes.AllelicCrosstalkCalibration	Non-documented_objects
getSetsOfProbes.ReseqCrosstalkCalibration	Non-documented_objects
getSettings	Non-documented_objects
getSettings.Package	Non-documented_objects
getSetTuple.ArrayExplorer	Non-documented_objects
getSignalTransform	Non-documented_objects
getSignalTransform.BasePositionNormalization	Non-documented_objects
getSignalTransform.LinearModelProbeSequenceNormalization	Non-documented_objects
getSnpInformation	Non-documented_objects
getSnpInformation.AffymetrixCdfFile	Non-documented_objects
getSnpNames	Non-documented_objects
getSnpNames,AffymetrixCdfFile-method	getSnpNames.AffymetrixCdfFile
getSnpNames.AffymetrixCdfFile	getSnpNames.AffymetrixCdfFile
getSpar	Non-documented_objects
getSpar.SpatialRowColumnNormalization	Non-documented_objects
getSteps	Non-documented_objects
getSteps.AromaPipeline	Non-documented_objects
getSteps.ASCRMAv2	Non-documented_objects
getSubsetOfCellIndices	Non-documented_objects
getSubsetOfCellIndices.AffymetrixCdfFile	Non-documented_objects
getSubsetOfUnits	Non-documented_objects
getSubsetOfUnits.AffymetrixCdfFile	Non-documented_objects
getSubsetToAvg	Non-documented_objects
getSubsetToAvg.AllelicCrosstalkCalibration	Non-documented_objects
getSubsetToAvg.QuantileNormalization	Non-documented_objects
getSubsetToAvg.ReseqCrosstalkCalibration	Non-documented_objects
getSubsetToAvg.ScaleNormalization	Non-documented_objects
getSubsetToFit	Non-documented_objects
getSubsetToFit.AdditiveCovariatesNormalization	Non-documented_objects
getSubsetToFit.FragmentEquivalentClassNormalization	Non-documented_objects
getSubsetToFit.FragmentLengthNormalization	Non-documented_objects
getSubsetToFit.GcContentNormalization	Non-documented_objects
getSubsetToUpdate	Non-documented_objects
getSubsetToUpdate.BackgroundCorrection	Non-documented_objects
getSubsetToUpdate.DChipQuantileNormalization	Non-documented_objects
getSubsetToUpdate.QuantileNormalization	Non-documented_objects
getSubsetToUpdate.ScaleNormalization	Non-documented_objects
getSubsetToUpdate0	Non-documented_objects
getSubsetToUpdate0.LimmaBackgroundCorrection	Non-documented_objects
getTags,GenericReporter-method	getTags.GenericReporter
getTags,Model-method	getTags.Model
getTags,TransformReport-method	getTags.TransformReport
getTags.FirmaModel	Non-documented_objects
getTags.GenericReporter	getTags.GenericReporter
getTags.Model	getTags.Model
getTags.QualityAssessmentModel	Non-documented_objects
getTags.TransformReport	getTags.TransformReport
getTagsOfInput.ArrayExplorer	Non-documented_objects
getTargetAverages	Non-documented_objects
getTargetAverages.FragmentEquivalentClassNormalization	Non-documented_objects
getTargetDistribution	Non-documented_objects
getTargetDistribution.QuantileNormalization	Non-documented_objects
getTargetDistributionIdentifier	Non-documented_objects
getTargetDistributionIdentifier.QuantileNormalization	Non-documented_objects
getTargetDistributionPathname	Non-documented_objects
getTargetDistributionPathname.QuantileNormalization	Non-documented_objects
getTargetFile	Non-documented_objects
getTargetFile.AbstractProbeSequenceNormalization	Non-documented_objects
getTargetFunction	Non-documented_objects
getTargetFunction.GcContentNormalization	Non-documented_objects
getTargetFunctions	Non-documented_objects
getTargetFunctions.AdditiveCovariatesNormalization	Non-documented_objects
getTargetFunctions.FragmentLengthNormalization	Non-documented_objects
getThetas	Non-documented_objects
getThetas.DChipDcpFile	Non-documented_objects
getThetasAB	Non-documented_objects
getThetasAB.DChipDcpFile	Non-documented_objects
getThetaStds	Non-documented_objects
getThetaStds.DChipDcpFile	Non-documented_objects
getTimeStamp	Non-documented_objects
getTimestamp	Non-documented_objects
getTimestamp,AffymetrixCelFile-method	getTimestamp.AffymetrixCelFile
getTimeStamp.AffymetrixAptSummaryFile	Non-documented_objects
getTimestamp.AffymetrixCelFile	getTimestamp.AffymetrixCelFile
getTimestamp.AffymetrixCnChpFile	Non-documented_objects
getTimestamp.CnagCfhFile	Non-documented_objects
getTimestamps	Non-documented_objects
getTimestamps.AffymetrixCelSet	Non-documented_objects
getTimestamps.CnagCfhSet	Non-documented_objects
getUnique	Non-documented_objects
getUnique.AffymetrixCdfFile	Non-documented_objects
getUniqueCdf	Non-documented_objects
getUniqueCdf.AffymetrixCdfFile	Non-documented_objects
getUnitGroupCellArrayMap	Non-documented_objects
getUnitGroupCellArrayMap.ChipEffectFile	Non-documented_objects
getUnitGroupCellChromosomePositionMap	Non-documented_objects
getUnitGroupCellChromosomePositionMap.AffymetrixCdfFile	Non-documented_objects
getUnitGroupCellChromosomePositionMap.ChipEffectFile	Non-documented_objects
getUnitGroupCellMap	Non-documented_objects
getUnitGroupCellMap,ChipEffectFile-method	getUnitGroupCellMap.ChipEffectFile
getUnitGroupCellMap.AffymetrixCdfFile	Non-documented_objects
getUnitGroupCellMap.AffymetrixCelSet	Non-documented_objects
getUnitGroupCellMap.ChipEffectFile	getUnitGroupCellMap.ChipEffectFile
getUnitGroupCellMap.FirmaFile	Non-documented_objects
getUnitGroupCellMap.ResidualFile	Non-documented_objects
getUnitGroupCellMap.WeightsFile	Non-documented_objects
getUnitGroupCellMapWithMonocell	Non-documented_objects
getUnitGroupCellMapWithMonocell.AffymetrixCdfFile	Non-documented_objects
getUnitGroupCellMapWithUnique	Non-documented_objects
getUnitGroupCellMapWithUnique.AffymetrixCdfFile	Non-documented_objects
getUnitGroupCellMatrixMap	Non-documented_objects
getUnitGroupCellMatrixMap.ChipEffectFile	Non-documented_objects
getUnitGroupNamesFromUgcMap	Non-documented_objects
getUnitGroupNamesFromUgcMap.AffymetrixCdfFile	Non-documented_objects
getUnitIndices	Non-documented_objects
getUnitIndices,GenomeInformation-method	getUnitIndices.GenomeInformation
getUnitIndices.GenomeInformation	getUnitIndices.GenomeInformation
getUnitIntensities	Non-documented_objects
getUnitIntensities,AffymetrixCelSet-method	getUnitIntensities.AffymetrixCelSet
getUnitIntensities.AffymetrixCelSet	getUnitIntensities.AffymetrixCelSet
getUnitNames,AffymetrixCdfFile-method	getUnitNames.AffymetrixCdfFile
getUnitNames.AffymetrixCdfFile	getUnitNames.AffymetrixCdfFile
getUnitNames.AffymetrixNetAffxCsvFile	Non-documented_objects
getUnitNames.DChipCdfBinFile	Non-documented_objects
getUnitNamesFile.AffymetrixCdfFile	Non-documented_objects
getUnitNamesFile.AffymetrixCelFile	Non-documented_objects
getUnitNamesFile.AffymetrixCelSet	Non-documented_objects
getUnitNamesFile.AffymetrixCnChpFile	Non-documented_objects
getUnitNamesFile.AffymetrixPlatform	Non-documented_objects
getUnitNamesFile.TransformReport	Non-documented_objects
getUnitReadMap	Non-documented_objects
getUnitReadMap.AffymetrixCnChpFile	Non-documented_objects
getUnitSizes	Non-documented_objects
getUnitSizes,AffymetrixCdfFile-method	nbrOfGroupsPerUnit.AffymetrixCdfFile
getUnitSizes.AffymetrixCdfFile	nbrOfGroupsPerUnit.AffymetrixCdfFile
getUnitSizes.DChipCdfBinFile	Non-documented_objects
getUnitsOnChromosome.GenomeInformation	Non-documented_objects
getUnitsOnChromosome.UgpGenomeInformation	Non-documented_objects
getUnitsOnChromosomes.GenomeInformation	Non-documented_objects
getUnitsTo	Non-documented_objects
getUnitsTo.ProbeLevelTransform3	Non-documented_objects
getUnitsToFit	Non-documented_objects
getUnitsToFit.CrlmmModel	Non-documented_objects
getUnitsToFit.ProbeLevelTransform3	Non-documented_objects
getUnitsToUpdate	Non-documented_objects
getUnitsToUpdate.ProbeLevelTransform3	Non-documented_objects
getUnitTypes,AffymetrixCdfFile-method	getUnitTypes.AffymetrixCdfFile
getUnitTypes.AffymetrixCdfFile	getUnitTypes.AffymetrixCdfFile
getUnitTypesFile.AffymetrixCdfFile	Non-documented_objects
getUnitTypesFile.AffymetrixCelFile	Non-documented_objects
getUnitTypesFile.AffymetrixCelSet	Non-documented_objects
getUnitTypesFile.AffymetrixCnChpFile	Non-documented_objects
getUnitTypesFile.AffymetrixPlatform	Non-documented_objects
getUnitTypesFile.TransformReport	Non-documented_objects
getWeights,QualityAssessmentModel-method	getWeights.QualityAssessmentModel
getWeights.QualityAssessmentModel	getWeights.QualityAssessmentModel
getWeightsFileClass	Non-documented_objects
getWeightsFileClass.WeightsSet	Non-documented_objects
getWeightsSet	Non-documented_objects
getWeightsSet.ProbeLevelModel	Non-documented_objects
getWeightsSetClass	Non-documented_objects
getWeightsSetClass.ProbeLevelModel	Non-documented_objects
getXAM,ChipEffectFile-method	getXAM.ChipEffectFile
getXAM,ChipEffectSet-method	getXAM.ChipEffectSet
getXAM.ChipEffectFile	getXAM.ChipEffectFile
getXAM.ChipEffectSet	getXAM.ChipEffectSet
getYY	Non-documented_objects
getYY.TransformReport	Non-documented_objects
groupUnitsByDimension	Non-documented_objects
groupUnitsByDimension,AffymetrixCdfFile-method	groupUnitsByDimension.AffymetrixCdfFile
groupUnitsByDimension.AffymetrixCdfFile	groupUnitsByDimension.AffymetrixCdfFile
hasAlleleBFractions.CnChipEffectFile	Non-documented_objects
hasAlleleBFractions.CnChipEffectSet	Non-documented_objects
hasAlleleBFractions.CnChipEffectSetTuple	Non-documented_objects
hasColumnHeader.AffymetrixProbeTabFile	Non-documented_objects
hasMbeiData	Non-documented_objects
hasMbeiData.DChipDcpFile	Non-documented_objects
hasNormalizedData	Non-documented_objects
hasNormalizedData.DChipDcpFile	Non-documented_objects
hasStrandiness.CnChipEffectFile	Non-documented_objects
hasStrandiness.CnChipEffectSet	Non-documented_objects
hasStrandiness.CnChipEffectSetTuple	Non-documented_objects
hasUnitReadMap	Non-documented_objects
hasUnitReadMap.AffymetrixCnChpFile	Non-documented_objects
hasUnitTypes	Non-documented_objects
hasUnitTypes.AffymetrixCdfFile	Non-documented_objects
HetLogAddCnPlm	HetLogAddCnPlm
HetLogAddPlm	HetLogAddPlm
HetLogAddPlm.getFitUnitGroupFunction	getFitUnitGroupFunction.HetLogAddPlm
HetLogAddSnpPlm	HetLogAddSnpPlm
highlight	Non-documented_objects
highlight.AffymetrixCelFile	Non-documented_objects
identifyCells	Non-documented_objects
identifyCells.AffymetrixCdfFile	Non-documented_objects
image270	Non-documented_objects
image270,AffymetrixCelFile-method	image270.AffymetrixCelFile
image270.AffymetrixCelFile	image270.AffymetrixCelFile
importFrom.AromaUnitTabularBinaryFile	Non-documented_objects
importFromAffymetrixNetAffxCsvFile	Non-documented_objects
importFromAffymetrixNetAffxCsvFile.AromaUflFile	Non-documented_objects
importFromAffymetrixNetAffxCsvFile.AromaUgpFile	Non-documented_objects
importFromAffymetrixNetAffxCsvFile.AromaUnitGcContentFile	Non-documented_objects
importFromAffymetrixNetAffxCsvFile.AromaUnitTabularBinaryFile	Non-documented_objects
importFromAffymetrixProbeTabFile	Non-documented_objects
importFromAffymetrixProbeTabFile.AromaCellSequenceFile	Non-documented_objects
importFromAffymetrixTabularFile	Non-documented_objects
importFromAffymetrixTabularFile.AromaUfcFile	Non-documented_objects
importFromAffymetrixTabularFile.AromaUgpFile	Non-documented_objects
importFromAffymetrixTabularFile.AromaUnitTabularBinaryFile	Non-documented_objects
importFromApt	Non-documented_objects
importFromApt,CnChipEffectSet-method	importFromApt.CnChipEffectSet
importFromApt.CnChipEffectSet	importFromApt.CnChipEffectSet
importFromBpMap	Non-documented_objects
importFromBpMap.AromaCellMatchScoreFile	Non-documented_objects
importFromBpMap.AromaCellSequenceFile	Non-documented_objects
importFromDChip	Non-documented_objects
importFromDChip,AffymetrixCelSet-method	importFromDChip.AffymetrixCelSet
importFromDChip,CnChipEffectSet-method	importFromDChip.CnChipEffectSet
importFromDChip.AffymetrixCelSet	importFromDChip.AffymetrixCelSet
importFromDChip.CnChipEffectSet	importFromDChip.CnChipEffectSet
importFromDChipGenomeInformation	Non-documented_objects
importFromDChipGenomeInformation.AromaUnitTabularBinaryFile	Non-documented_objects
importFromGenericTabularFile.AromaUnitTabularBinaryFile	Non-documented_objects
importFromGenomeInformation	Non-documented_objects
importFromGenomeInformation.AromaUgpFile	Non-documented_objects
importFromGenomeInformation.AromaUnitTabularBinaryFile	Non-documented_objects
indexOfMissingSequences	Non-documented_objects
indexOfMissingSequences.AbstractProbeSequenceNormalization	Non-documented_objects
inferMmFromPm	Non-documented_objects
inferMmFromPm.AromaCellSequenceFile	Non-documented_objects
inferParameters	Non-documented_objects
inferParameters.CnChipEffectSet	Non-documented_objects
inferParameters.SnpChipEffectSet	Non-documented_objects
isCompatibleWithCdf	Non-documented_objects
isCompatibleWithCdf.GenomeInformation	Non-documented_objects
isCompatibleWithCdf.SnpInformation	Non-documented_objects
isCompatibleWithCdf.UflSnpInformation	Non-documented_objects
isCompatibleWithCdf.UgpGenomeInformation	Non-documented_objects
isDuplicated	Non-documented_objects
isDuplicated,AffymetrixCelSet-method	isDuplicated.AffymetrixCelSet
isDuplicated,CnagCfhSet-method	isDuplicated.CnagCfhSet
isDuplicated.AffymetrixCelSet	isDuplicated.AffymetrixCelSet
isDuplicated.CnagCfhSet	isDuplicated.CnagCfhSet
isMissing.AromaCellMatchScoreFile	Non-documented_objects
isMonocellCdf	Non-documented_objects
isMonocellCdf.AffymetrixCdfFile	Non-documented_objects
isPm	Non-documented_objects
isPm,AffymetrixCdfFile-method	isPm.AffymetrixCdfFile
isPm.AffymetrixCdfFile	isPm.AffymetrixCdfFile
isResequenceChip	Non-documented_objects
isResequenceChip,AffymetrixCdfFile-method	isResequenceChip.AffymetrixCdfFile
isResequenceChip.AffymetrixCdfFile	isResequenceChip.AffymetrixCdfFile
isSnpChip	Non-documented_objects
isSnpChip,AffymetrixCdfFile-method	isSnpChip.AffymetrixCdfFile
isSnpChip.AffymetrixCdfFile	isSnpChip.AffymetrixCdfFile
isUniqueCdf	Non-documented_objects
isUniqueCdf.AffymetrixCdfFile	Non-documented_objects
isUnitGroupCellMap	Non-documented_objects
isUnitGroupCellMap.data.frame	Non-documented_objects
isUnitGroupCellMap.default	Non-documented_objects
isUnitGroupCellMap.matrix	Non-documented_objects
justSNPRMA	Non-documented_objects
justSNPRMA.AffymetrixCelSet	Non-documented_objects
justSNPRMA.character	Non-documented_objects
lapply	Non-documented_objects
library	Non-documented_objects
LimmaBackgroundCorrection	LimmaBackgroundCorrection
LimmaBackgroundCorrection.process	process.LimmaBackgroundCorrection
LinearModelProbeSequenceNormalization	LinearModelProbeSequenceNormalization
mapToUnitNamesFile	Non-documented_objects
mapToUnitNamesFile.DChipCdfBinFile	Non-documented_objects
MatNormalization	MatNormalization
MatNormalization.process	process.MatNormalization
MatSmoothing	MatSmoothing
MatSmoothing.process	process.MatSmoothing
MbeiCnPlm	MbeiCnPlm
MbeiPlm	MbeiPlm
MbeiPlm.getFitUnitGroupFunction	getFitUnitGroupFunction.MbeiPlm
MbeiSnpPlm	MbeiSnpPlm
mergeGroups	Non-documented_objects
mergeGroups.ChipEffectFile	Non-documented_objects
mergeStrands	Non-documented_objects
mergeStrands.CnChipEffectFile	Non-documented_objects
mergeStrands.SnpChipEffectFile	Non-documented_objects
migrateTool	Non-documented_objects
migrateTool.CopyNumberSegmentationModel	Non-documented_objects
Model	Model
Model.fit	fit.Model
Model.getAlias	getAlias.Model
Model.getCdf	getCdf.Model
Model.getDataSet	getDataSet.Model
Model.getFullName	getFullName.Model
Model.getName	getName.Model
Model.getPath	getPath.Model
Model.getRootPath	getRootPath.Model
Model.getTags	getTags.Model
Model.setAlias	setAlias.Model
Model.setTags	setTags.Model
MultiArrayUnitModel	MultiArrayUnitModel
MultiArrayUnitModel.getFitUnitGroupFunction	getFitUnitGroupFunction.MultiArrayUnitModel
MultiArrayUnitModel.readUnits	readUnits.MultiArrayUnitModel
nbrOfArrays,AffymetrixCelSet-method	nbrOfArrays.AffymetrixCelSet
nbrOfArrays,AffymetrixCnChpSet-method	nbrOfArrays.AffymetrixCnChpSet
nbrOfArrays,CnagCfhSet-method	nbrOfArrays.CnagCfhSet
nbrOfArrays,DChipDcpSet-method	nbrOfArrays.DChipDcpSet
nbrOfArrays.AffymetrixAptSummaryFile	Non-documented_objects
nbrOfArrays.AffymetrixCelSet	nbrOfArrays.AffymetrixCelSet
nbrOfArrays.AffymetrixCelSetReporter	Non-documented_objects
nbrOfArrays.AffymetrixCnChpSet	nbrOfArrays.AffymetrixCnChpSet
nbrOfArrays.CnagCfhSet	nbrOfArrays.CnagCfhSet
nbrOfArrays.DChipDcpSet	nbrOfArrays.DChipDcpSet
nbrOfArrays.QualityAssessmentModel	Non-documented_objects
nbrOfArrays.TransformReport	Non-documented_objects
nbrOfCells.AffymetrixCdfFile	Non-documented_objects
nbrOfCells.AffymetrixCelFile	Non-documented_objects
nbrOfCells.CnagCfhFile	Non-documented_objects
nbrOfCells.DChipCdfBinFile	Non-documented_objects
nbrOfCells.DChipDcpFile	Non-documented_objects
nbrOfCellsPerUnit	Non-documented_objects
nbrOfCellsPerUnit.AffymetrixCdfFile	Non-documented_objects
nbrOfCellsPerUnitGroup	Non-documented_objects
nbrOfCellsPerUnitGroup.AffymetrixCdfFile	Non-documented_objects
nbrOfChipTypes.ArrayExplorer	Non-documented_objects
nbrOfColumns.AffymetrixCdfFile	Non-documented_objects
nbrOfEnzymes.AromaUfcFile	Non-documented_objects
nbrOfEnzymes.SnpInformation	Non-documented_objects
nbrOfEnzymes.UflSnpInformation	Non-documented_objects
nbrOfGroupsPerUnit	Non-documented_objects
nbrOfGroupsPerUnit,AffymetrixCdfFile-method	nbrOfGroupsPerUnit.AffymetrixCdfFile
nbrOfGroupsPerUnit.AffymetrixCdfFile	nbrOfGroupsPerUnit.AffymetrixCdfFile
nbrOfQcUnits	Non-documented_objects
nbrOfQcUnits.AffymetrixCdfFile	Non-documented_objects
nbrOfRows.AffymetrixCdfFile	Non-documented_objects
nbrOfSnps	Non-documented_objects
nbrOfSnps,AffymetrixCdfFile-method	nbrOfSnps.AffymetrixCdfFile
nbrOfSnps.AffymetrixCdfFile	nbrOfSnps.AffymetrixCdfFile
nbrOfSnps.CnagCfhFile	Non-documented_objects
nbrOfSteps	Non-documented_objects
nbrOfSteps.AromaPipeline	Non-documented_objects
nbrOfUnits.AffymetrixCdfFile	Non-documented_objects
nbrOfUnits.DChipCdfBinFile	Non-documented_objects
nbrOfUnits.DChipDcpFile	Non-documented_objects
nbrOfUnits.GenomeInformation	Non-documented_objects
nbrOfUnits.SnpInformation	Non-documented_objects
nbrOfUnits.UflSnpInformation	Non-documented_objects
nbrOfUnits.UgpGenomeInformation	Non-documented_objects
Non-documented objects	Non-documented_objects
normalizeOneArrayVector	Non-documented_objects
normalizeOneArrayVector.FragmentEquivalentClassNormalization	Non-documented_objects
normalizeQuantile,AffymetrixCelFile-method	normalizeQuantile.AffymetrixCelFile
normalizeQuantile,AffymetrixCelSet-method	normalizeQuantile.AffymetrixCelSet
normalizeQuantile.AffymetrixCelFile	normalizeQuantile.AffymetrixCelFile
normalizeQuantile.AffymetrixCelSet	normalizeQuantile.AffymetrixCelSet
NormExpBackgroundCorrection	NormExpBackgroundCorrection
OpticalBackgroundCorrection	OpticalBackgroundCorrection
OpticalBackgroundCorrection.process	process.OpticalBackgroundCorrection
ParameterCelFile	ParameterCelFile
ParameterCelSet	ParameterCelSet
ParameterCelSet.extractDataFrame	extractDataFrame.ParameterCelSet
ParameterCelSet.extractMatrix	extractMatrix.ParameterCelSet
patch.AromaAffymetrix	Non-documented_objects
PdInfo2Cdf	pdInfo2Cdf
pdInfo2Cdf	pdInfo2Cdf
plasqGaussian	Non-documented_objects
plotAllelePairs	Non-documented_objects
plotAllelePairs.AllelicCrosstalkCalibration	Non-documented_objects
plotBasepair	Non-documented_objects
plotBasepair.AllelicCrosstalkCalibration	Non-documented_objects
plotBoxplot	Non-documented_objects
plotBoxplot.ChipEffectSet	Non-documented_objects
plotBoxplotStats	Non-documented_objects
plotBoxplotStats.list	plotBoxplotStats.list
plotCovariateEffects	Non-documented_objects
plotCovariateEffects.GcContentNormalization2	Non-documented_objects
plotDensity,AffymetrixCelFile-method	plotDensity.AffymetrixCelFile
plotDensity,AffymetrixCelSet-method	plotDensity.AffymetrixCelSet
plotDensity,GenomeInformation-method	plotDensity.GenomeInformation
plotDensity.AffymetrixCelFile	plotDensity.AffymetrixCelFile
plotDensity.AffymetrixCelSet	plotDensity.AffymetrixCelSet
plotDensity.GenomeInformation	plotDensity.GenomeInformation
plotImage	Non-documented_objects
plotImage,AffymetrixCelFile-method	plotImage.AffymetrixCelFile
plotImage.AffymetrixCelFile	plotImage.AffymetrixCelFile
plotMargins	Non-documented_objects
plotMargins.SpatialReporter	Non-documented_objects
plotMvsA,AffymetrixCelFile-method	plotMvsA.AffymetrixCelFile
plotMvsA.AffymetrixCelFile	plotMvsA.AffymetrixCelFile
plotMvsX	Non-documented_objects
plotMvsX,AffymetrixCelFile-method	plotMvsX.AffymetrixCelFile
plotMvsX.AffymetrixCelFile	plotMvsX.AffymetrixCelFile
plotNuse	Non-documented_objects
plotNuse.QualityAssessmentModel	Non-documented_objects
plotRle	Non-documented_objects
plotRle.QualityAssessmentModel	Non-documented_objects
plotXYCurve.TransformReport	Non-documented_objects
plotXYCurveLog2	Non-documented_objects
plotXYCurveLog2.TransformReport	Non-documented_objects
predictOne	Non-documented_objects
predictOne.AbstractProbeSequenceNormalization	Non-documented_objects
predictOne.BaseCountNormalization	Non-documented_objects
predictOne.LinearModelProbeSequenceNormalization	Non-documented_objects
predictOne.MatNormalization	Non-documented_objects
ProbeAffinityFile	ProbeAffinityFile
ProbeLevelModel	ProbeLevelModel
ProbeLevelModel.findUnitsTodo	findUnitsTodo.ProbeLevelModel
ProbeLevelModel.fit	fit.ProbeLevelModel
ProbeLevelModel.getChipEffects	getChipEffectSet.ProbeLevelModel
ProbeLevelModel.getChipEffectSet	getChipEffectSet.ProbeLevelModel
ProbeLevelModel.getProbeAffinities	getProbeAffinityFile.ProbeLevelModel
ProbeLevelModel.getProbeAffinityFile	getProbeAffinityFile.ProbeLevelModel
ProbeLevelTransform	ProbeLevelTransform
ProbeLevelTransform3	ProbeLevelTransform3
process,AbstractProbeSequenceNormalization-method	process.AbstractProbeSequenceNormalization
process,AdditiveCovariatesNormalization-method	process.AdditiveCovariatesNormalization
process,AllelicCrosstalkCalibration-method	process.AllelicCrosstalkCalibration
process,ArrayExplorer-method	process.ArrayExplorer
process,BackgroundCorrection-method	process.BackgroundCorrection
process,ChipEffectGroupMerge-method	process.ChipEffectGroupMerge
process,DChipQuantileNormalization-method	process.DChipQuantileNormalization
process,FragmentEquivalentClassNormalization-method	process.FragmentEquivalentClassNormalization
process,FragmentLengthNormalization-method	process.FragmentLengthNormalization
process,GcContentNormalization-method	process.GcContentNormalization
process,GcRmaBackgroundCorrection-method	process.GcRmaBackgroundCorrection
process,GenericReporter-method	process.GenericReporter
process,LimmaBackgroundCorrection-method	process.LimmaBackgroundCorrection
process,MatNormalization-method	process.MatNormalization
process,MatSmoothing-method	process.MatSmoothing
process,OpticalBackgroundCorrection-method	process.OpticalBackgroundCorrection
process,QuantileNormalization-method	process.QuantileNormalization
process,ReseqCrosstalkCalibration-method	process.ReseqCrosstalkCalibration
process,RmaBackgroundCorrection-method	process.RmaBackgroundCorrection
process,ScaleNormalization-method	process.ScaleNormalization
process,ScaleNormalization3-method	process.ScaleNormalization3
process,SpatialReporter-method	process.SpatialReporter
process,UnitTypeScaleNormalization-method	process.UnitTypeScaleNormalization
process.AbstractProbeSequenceNormalization	process.AbstractProbeSequenceNormalization
process.AdditiveCovariatesNormalization	process.AdditiveCovariatesNormalization
process.AlleleSummation	Non-documented_objects
process.AllelicCrosstalkCalibration	process.AllelicCrosstalkCalibration
process.AromaPipeline	Non-documented_objects
process.ArrayExplorer	process.ArrayExplorer
process.BackgroundCorrection	process.BackgroundCorrection
process.ChipEffectGroupMerge	process.ChipEffectGroupMerge
process.DChipQuantileNormalization	process.DChipQuantileNormalization
process.FragmentEquivalentClassNormalization	process.FragmentEquivalentClassNormalization
process.FragmentLengthNormalization	process.FragmentLengthNormalization
process.GcContentNormalization	process.GcContentNormalization
process.GcRmaBackgroundCorrection	process.GcRmaBackgroundCorrection
process.GenericReporter	process.GenericReporter
process.LimmaBackgroundCorrection	process.LimmaBackgroundCorrection
process.MatNormalization	process.MatNormalization
process.MatSmoothing	process.MatSmoothing
process.OpticalBackgroundCorrection	process.OpticalBackgroundCorrection
process.QuantileNormalization	process.QuantileNormalization
process.ReseqCrosstalkCalibration	process.ReseqCrosstalkCalibration
process.RmaBackgroundCorrection	process.RmaBackgroundCorrection
process.ScaleNormalization	process.ScaleNormalization
process.ScaleNormalization3	process.ScaleNormalization3
process.SpatialReporter	process.SpatialReporter
process.SpatialRowColumnNormalization	Non-documented_objects
process.UnitTypeScaleNormalization	process.UnitTypeScaleNormalization
QualityAssessmentFile	QualityAssessmentFile
QualityAssessmentModel	QualityAssessmentModel
QualityAssessmentModel.getResiduals	getResiduals.QualityAssessmentModel
QualityAssessmentModel.getWeights	getWeights.QualityAssessmentModel
QualityAssessmentSet	QualityAssessmentSet
QuantileNormalization	QuantileNormalization
QuantileNormalization.process	process.QuantileNormalization
range.AffymetrixCelFile	Non-documented_objects
range.AffymetrixCelSet	Non-documented_objects
range.CnagCfhFile	Non-documented_objects
range.CnagCfhSet	Non-documented_objects
read10K	Non-documented_objects
read10K.DChipSnpInformation	Non-documented_objects
read250K	Non-documented_objects
read250K.DChipSnpInformation	Non-documented_objects
read250KHg17	Non-documented_objects
read250KHg17.DChipGenomeInformation	Non-documented_objects
read50K	Non-documented_objects
read50K.DChipSnpInformation	Non-documented_objects
read50KHg17	Non-documented_objects
read50KHg17.DChipGenomeInformation	Non-documented_objects
readArrays	Non-documented_objects
readArrays.AffymetrixAptSummaryFile	Non-documented_objects
readCdfDataFrame	readCdfDataFrame
readCdfGroupStrands	Non-documented_objects
readCfhHeader	Non-documented_objects
readCfhHeader.default	Non-documented_objects
readCfhUnits	Non-documented_objects
readCfhUnits.default	Non-documented_objects
readCfnHeader	Non-documented_objects
readCfnHeader.default	Non-documented_objects
readCfnUnits	Non-documented_objects
readCfnUnits.default	Non-documented_objects
readData.AffymetrixTsvFile	Non-documented_objects
readData.GenomeInformation	Non-documented_objects
readData.SnpInformation	Non-documented_objects
readDataFrame.AffymetrixCdfFile	Non-documented_objects
readDataFrame.AffymetrixCsvGenomeInformation	Non-documented_objects
readDataFrame.AffymetrixTsvFile	Non-documented_objects
readDataFrame.AromaUfcFile	Non-documented_objects
readDataFrame.DChipCdfBinFile	Non-documented_objects
readDataFrame.DChipGenomeInformation	Non-documented_objects
readDataFrame.DChipSnpInformation	Non-documented_objects
readDataFrame.GenomeInformation	Non-documented_objects
readDataFrame.SnpInformation	Non-documented_objects
readDataFrame.UflSnpInformation	Non-documented_objects
readDataFrame.UgpGenomeInformation	Non-documented_objects
readDataFrame2	Non-documented_objects
readDataFrame2.AffymetrixProbeTabFile	Non-documented_objects
readDataUnitChromosomePosition	Non-documented_objects
readDataUnitChromosomePosition.AffymetrixNetAffxCsvFile	Non-documented_objects
readDataUnitFragmentLength	Non-documented_objects
readDataUnitFragmentLength.AffymetrixNetAffxCsvFile	Non-documented_objects
readGeneAssignments	Non-documented_objects
readGeneAssignments.AffymetrixNetAffxCsvFile	Non-documented_objects
readGenomeWideSNP	Non-documented_objects
readGenomeWideSNP.DChipGenomeInformation	Non-documented_objects
readHeader.AffymetrixAptSummaryFile	Non-documented_objects
readMatchScores	Non-documented_objects
readMatchScores.AromaCellMatchScoreFile	Non-documented_objects
readMouse430	Non-documented_objects
readMouse430.DChipGenomeInformation	Non-documented_objects
readMouse430KenHardwired	Non-documented_objects
readMouse430KenHardwired.DChipGenomeInformation	Non-documented_objects
readParameter	Non-documented_objects
readParameter.CrlmmParametersFile	Non-documented_objects
readPlasqTypes	Non-documented_objects
readPlasqTypes.AffymetrixCdfFile	Non-documented_objects
readPriorsByUnits	Non-documented_objects
readPriorsByUnits.MultiArrayUnitModel	Non-documented_objects
readProbesetIds	Non-documented_objects
readProbesetIds.AffymetrixAptSummaryFile	Non-documented_objects
readRawData	Non-documented_objects
readRawData,AffymetrixCelFile-method	readRawData.AffymetrixCelFile
readRawData.AffymetrixCelFile	readRawData.AffymetrixCelFile
readRawData.AffymetrixCnChpFile	Non-documented_objects
readRawDataRectangle	Non-documented_objects
readRawDataRectangle.AffymetrixCelFile	Non-documented_objects
readRawDataRectangle.SpatialReporter	Non-documented_objects
readSequenceDataFrame	Non-documented_objects
readSequenceDataFrame.AffymetrixProbeTabFile	Non-documented_objects
readTableInternal	Non-documented_objects
readTableInternal.GenomeInformation	Non-documented_objects
readTableInternal.SnpInformation	Non-documented_objects
readUnitNames	Non-documented_objects
readUnitNames.AffymetrixNetAffxCsvFile	Non-documented_objects
readUnits	Non-documented_objects
readUnits,AffymetrixCdfFile-method	readUnits.AffymetrixCdfFile
readUnits,AffymetrixCelFile-method	readUnits.AffymetrixCelFile
readUnits,CnagCfhFile-method	readUnits.CnagCfhFile
readUnits,MultiArrayUnitModel-method	readUnits.MultiArrayUnitModel
readUnits,SingleArrayUnitModel-method	readUnits.SingleArrayUnitModel
readUnits.AffymetrixCdfFile	readUnits.AffymetrixCdfFile
readUnits.AffymetrixCelFile	readUnits.AffymetrixCelFile
readUnits.AffymetrixCelSet	Non-documented_objects
readUnits.ChipEffectFile	Non-documented_objects
readUnits.ChipEffectSet	Non-documented_objects
readUnits.CnagCfhFile	readUnits.CnagCfhFile
readUnits.CnagCfhSet	Non-documented_objects
readUnits.CnChipEffectFile	Non-documented_objects
readUnits.ExonChipEffectFile	Non-documented_objects
readUnits.FirmaFile	Non-documented_objects
readUnits.FirmaSet	Non-documented_objects
readUnits.MultiArrayUnitModel	readUnits.MultiArrayUnitModel
readUnits.ParameterCelFile	Non-documented_objects
readUnits.ProbeAffinityFile	Non-documented_objects
readUnits.ResidualFile	Non-documented_objects
readUnits.ResidualSet	Non-documented_objects
readUnits.SingleArrayUnitModel	readUnits.SingleArrayUnitModel
readUnits.SnpChipEffectFile	Non-documented_objects
readUnits.WeightsFile	Non-documented_objects
readUnits.WeightsSet	Non-documented_objects
readUnitsByQuartets	Non-documented_objects
readUnitsByQuartets,AffymetrixCdfFile-method	readUnitsByQuartets.AffymetrixCdfFile
readUnitsByQuartets.AffymetrixCdfFile	readUnitsByQuartets.AffymetrixCdfFile
require	Non-documented_objects
rescale.AllelicCrosstalkCalibration	Non-documented_objects
rescaleByAll	Non-documented_objects
rescaleByAll.AllelicCrosstalkCalibration	Non-documented_objects
rescaleByAll.ReseqCrosstalkCalibration	Non-documented_objects
rescaleByGroups	Non-documented_objects
rescaleByGroups.AllelicCrosstalkCalibration	Non-documented_objects
ReseqCrosstalkCalibration	ReseqCrosstalkCalibration
ReseqCrosstalkCalibration.process	process.ReseqCrosstalkCalibration
ResidualFile	ResidualFile
ResidualSet	ResidualSet
restruct	Non-documented_objects
restruct.AffymetrixCdfFile	Non-documented_objects
RmaBackgroundCorrection	RmaBackgroundCorrection
RmaBackgroundCorrection.process	process.RmaBackgroundCorrection
RmaCnPlm	RmaCnPlm
RmaPlm	RmaPlm
RmaPlm.getFitUnitGroupFunction	getFitUnitGroupFunction.RmaPlm
RmaSnpPlm	RmaSnpPlm
sapply	Non-documented_objects
ScaleNormalization	ScaleNormalization
ScaleNormalization.process	process.ScaleNormalization
ScaleNormalization3	ScaleNormalization3
ScaleNormalization3.process	process.ScaleNormalization3
seq.TransformReport	Non-documented_objects
setAlias,GenericReporter-method	setAlias.GenericReporter
setAlias,Model-method	setAlias.Model
setAlias.ArrayExplorer	Non-documented_objects
setAlias.GenericReporter	setAlias.GenericReporter
setAlias.Model	setAlias.Model
setAlias.TransformReport	Non-documented_objects
setArrays,ArrayExplorer-method	setArrays.ArrayExplorer
setArrays.ArrayExplorer	setArrays.ArrayExplorer
setBandwidth	Non-documented_objects
setBandwidth.SmoothMultiarrayModel	Non-documented_objects
setCdf	Non-documented_objects
setCdf,AffymetrixCelFile-method	setCdf.AffymetrixCelFile
setCdf,AffymetrixCelSet-method	setCdf.AffymetrixCelSet
setCdf,CnagCfhFile-method	setCdf.CnagCfhFile
setCdf,CnagCfhSet-method	setCdf.CnagCfhSet
setCdf.AffymetrixCelFile	setCdf.AffymetrixCelFile
setCdf.AffymetrixCelSet	setCdf.AffymetrixCelSet
setCdf.AffymetrixCnChpFile	Non-documented_objects
setCdf.AffymetrixCnChpSet	Non-documented_objects
setCdf.CnagCfhFile	setCdf.CnagCfhFile
setCdf.CnagCfhSet	setCdf.CnagCfhSet
setColorMaps	Non-documented_objects
setColorMaps.ArrayExplorer	Non-documented_objects
setColorMaps.SpatialReporter	Non-documented_objects
setCombineAlleles	Non-documented_objects
setCombineAlleles.CnChipEffectSet	Non-documented_objects
setCombineAlleles.CnPlm	Non-documented_objects
setCombineAlleles.CnProbeAffinityFile	Non-documented_objects
setCustomFindCdf	Non-documented_objects
setDecodeFunction	Non-documented_objects
setDecodeFunction.ParameterCelFile	Non-documented_objects
setEncodeFunction	Non-documented_objects
setEncodeFunction.ParameterCelFile	Non-documented_objects
setGenomeInformation	Non-documented_objects
setGenomeInformation.AffymetrixCdfFile	Non-documented_objects
setLabel.Model	Non-documented_objects
setListOfPriors	Non-documented_objects
setListOfPriors.MultiArrayUnitModel	Non-documented_objects
setMergeFunction	Non-documented_objects
setMergeFunction.ChipEffectGroupMerge	Non-documented_objects
setMergeGroups	Non-documented_objects
setMergeGroups.ExonChipEffectSet	Non-documented_objects
setMergeGroups.ExonProbeAffinityFile	Non-documented_objects
setMergeGroups.ExonRmaPlm	Non-documented_objects
setMergeStrands	Non-documented_objects
setMergeStrands.SnpChipEffectSet	Non-documented_objects
setMergeStrands.SnpPlm	Non-documented_objects
setMergeStrands.SnpProbeAffinityFile	Non-documented_objects
setReference	Non-documented_objects
setReference.SpatialReporter	Non-documented_objects
setRestructor	Non-documented_objects
setRestructor,AffymetrixCdfFile-method	setRestructor.AffymetrixCdfFile
setRestructor.AffymetrixCdfFile	setRestructor.AffymetrixCdfFile
setSettings	Non-documented_objects
setSettings.Package	Non-documented_objects
setSnpInformation	Non-documented_objects
setSnpInformation.AffymetrixCdfFile	Non-documented_objects
setTags,Model-method	setTags.Model
setTags.Model	setTags.Model
setUnitReadMap	Non-documented_objects
setUnitReadMap.AffymetrixCnChpFile	Non-documented_objects
setup.ArrayExplorer	Non-documented_objects
setup.GenericReporter	Non-documented_objects
SingleArrayUnitModel	SingleArrayUnitModel
SingleArrayUnitModel.fit	fit.SingleArrayUnitModel
SingleArrayUnitModel.getFitUnitGroupFunction	getFitUnitGroupFunction.SingleArrayUnitModel
SingleArrayUnitModel.readUnits	readUnits.SingleArrayUnitModel
SmoothMultiarrayModel	SmoothMultiarrayModel
SmoothMultiarrayModel.fit	fit.SmoothMultiarrayModel
SmoothRmaModel	SmoothRmaModel
SmoothSaModel	Non-documented_objects
smoothScatterMvsA	Non-documented_objects
smoothScatterMvsA,AffymetrixCelFile-method	smoothScatterMvsA.AffymetrixCelFile
smoothScatterMvsA.AffymetrixCelFile	smoothScatterMvsA.AffymetrixCelFile
SnpChipEffectFile	SnpChipEffectFile
SnpChipEffectGroupMerge	SnpChipEffectGroupMerge
SnpChipEffectSet	SnpChipEffectSet
SnpInformation	SnpInformation
SnpInformation.byChipType	byChipType.SnpInformation
SnpInformation.fromCdf	fromCdf.SnpInformation
SnpInformation.getChipType	getChipType.SnpInformation
SnpInformation.getData	getData.SnpInformation
SnpInformation.verify	verify.SnpInformation
SnpPlm	SnpPlm
SnpProbeAffinityFile	SnpProbeAffinityFile
SpatialReporter	SpatialReporter
SpatialReporter.process	process.SpatialReporter
SpatialRowColumnNormalization	Non-documented_objects
stextChipType.AffymetrixCdfFile	Non-documented_objects
Transform	Non-documented_objects
Transform.getOutputDataSet	getOutputDataSet.Transform
transformAffine	Non-documented_objects
transformAffine.AffymetrixCelFile	Non-documented_objects
transformAffine.AffymetrixCelSet	Non-documented_objects
TransformReport	TransformReport
TransformReport.getFullName	getFullName.TransformReport
TransformReport.getInputDataSet	getInputDataSet.TransformReport
TransformReport.getName	getName.TransformReport
TransformReport.getOutputDataSet	getOutputDataSet.TransformReport
TransformReport.getPath	getPath.TransformReport
TransformReport.getTags	getTags.TransformReport
translateColumnNames.AffymetrixAptSummaryFile	Non-documented_objects
translateColumnNames.AffymetrixProbeTabFile	Non-documented_objects
translateColumnNames.AffymetrixTabularFile	Non-documented_objects
translateFullName.AffymetrixProbeTabFile	Non-documented_objects
UflSnpInformation	Non-documented_objects
UgpGenomeInformation	UgpGenomeInformation
UgpGenomeInformation.byChipType	byChipType.UgpGenomeInformation
UnitModel	UnitModel
UnitModel.findUnitsTodo	findUnitsTodo.UnitModel
UnitModel.getCellIndices	getCellIndices.UnitModel
UnitTypeScaleNormalization	UnitTypeScaleNormalization
UnitTypeScaleNormalization.process	process.UnitTypeScaleNormalization
update.AromaAffymetrix	Non-documented_objects
update2.AffymetrixCelSet	Non-documented_objects
updateDataFlat	Non-documented_objects
updateDataFlat.ChipEffectFile	Non-documented_objects
updateDataFlat.FirmaFile	Non-documented_objects
updateDataFlat.ResidualFile	Non-documented_objects
updateDataFlat.WeightsFile	Non-documented_objects
updateMatchScores	Non-documented_objects
updateMatchScores.AromaCellMatchScoreFile	Non-documented_objects
updateOnChipTypeJS	Non-documented_objects
updateOnChipTypeJS.ArrayExplorer	Non-documented_objects
updateOnLoadJS	Non-documented_objects
updateOnLoadJS.ArrayExplorer	Non-documented_objects
updateParameter	Non-documented_objects
updateParameter.CrlmmParametersFile	Non-documented_objects
updateSampleAnnotationSet	Non-documented_objects
updateSampleAnnotationSet.AffymetrixCelSet	Non-documented_objects
updateSettings	Non-documented_objects
updateSettings.Package	Non-documented_objects
updateUnits	Non-documented_objects
updateUnits,AffymetrixCelFile-method	updateUnits.AffymetrixCelFile
updateUnits.AffymetrixCelFile	updateUnits.AffymetrixCelFile
updateUnits.ChipEffectFile	Non-documented_objects
updateUnits.ChipEffectSet	Non-documented_objects
updateUnits.FirmaFile	Non-documented_objects
updateUnits.FirmaSet	Non-documented_objects
updateUnits.ParameterCelFile	Non-documented_objects
updateUnits.ProbeAffinityFile	Non-documented_objects
updateUnits.ResidualFile	Non-documented_objects
updateUnits.ResidualSet	Non-documented_objects
updateUnits.WeightsFile	Non-documented_objects
updateUnits.WeightsSet	Non-documented_objects
validate.AvgPlm	Non-documented_objects
validate.MultiArrayUnitModel	Non-documented_objects
verify,GenomeInformation-method	verify.GenomeInformation
verify,SnpInformation-method	verify.SnpInformation
verify.AffymetrixCsvGenomeInformation	Non-documented_objects
verify.AffymetrixTsvFile	Non-documented_objects
verify.DChipGenomeInformation	Non-documented_objects
verify.DChipSnpInformation	Non-documented_objects
verify.GenomeInformation	verify.GenomeInformation
verify.SnpInformation	verify.SnpInformation
verify.UflSnpInformation	Non-documented_objects
verify.UgpGenomeInformation	Non-documented_objects
WeightsFile	WeightsFile
WeightsSet	WeightsSet
write	Non-documented_objects
writeAsFullCelFile	Non-documented_objects
writeAsFullCelFile.ChipEffectFile	Non-documented_objects
writeCdf	Non-documented_objects
writeCdf,AffyGenePDInfo-method	writeCdf.AffyGenePDInfo
writeCdf.AffyGenePDInfo	writeCdf.AffyGenePDInfo
writeCdf.default	Non-documented_objects
writeCdfByExcludingCells	Non-documented_objects
writeCdfByExcludingCells.AffymetrixCdfFile	Non-documented_objects
writeCNT	Non-documented_objects
writeCNT.SnpChipEffectFile	Non-documented_objects
writeCNT.SnpChipEffectSet	Non-documented_objects
writeImage	Non-documented_objects
writeImage,AffymetrixCelFile-method	writeImage.AffymetrixCelFile
writeImage.AffymetrixCelFile	writeImage.AffymetrixCelFile
writeImage.ResidualFile	Non-documented_objects
writeImage.WeightsFile	Non-documented_objects
writeImageCombined	Non-documented_objects
writeImageCombined.TransformReport	Non-documented_objects
writeImages	Non-documented_objects
writeImages.SpatialReporter	Non-documented_objects
writeImages.TransformReport	Non-documented_objects
writeRegions.profileCGH	Non-documented_objects
writeSgr	Non-documented_objects
writeSgr.AffymetrixCelSet	Non-documented_objects
writeSignals	Non-documented_objects
writeSignals.ProbeLevelTransform3	Non-documented_objects
writeWig	Non-documented_objects
writeWig.CnChipEffectSet	Non-documented_objects
[.AffymetrixCelFile	Non-documented_objects
[.AffymetrixCelSet	Non-documented_objects
[.CnagCfhFile	Non-documented_objects
[.CnagCfhSet	Non-documented_objects
[[.AffymetrixCelFile	Non-documented_objects
[[.AffymetrixCelSet	Non-documented_objects
[[.CnagCfhFile	Non-documented_objects
[[.CnagCfhSet	Non-documented_objects
