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

