  [.AffymetrixCelFile [.AffymetrixCelSet [.CnagCfhFile [.CnagCfhSet
  [[.AffymetrixCelFile [[.AffymetrixCelSet [[.CnagCfhFile [[.CnagCfhSet
  addColorMap addColorMap.ArrayExplorer addColorMap.ChipTypeReporter
  addColorMap.SpatialReporter addExclCells
  addExclCells.DChipQuantileNormalization addIncludes
  addIncludes.Explorer addIndexFile addIndexFile.ChromosomeExplorer
  addIndexFile.Explorer AffymetrixAptSummaryFile AffymetrixCnChpFile
  AffymetrixCsvFile AffymetrixCsvGenomeInformation
  AffymetrixNetAffxCsvFile AffymetrixPlatform AffymetrixTabularFile
  AffymetrixTsvFile allocateFromCdf allocateFromCdf.AromaUfcFile
  allocateFromCdf.AromaUflFile allocateFromCdf.AromaUgpFile
  annotateMvsA annotateMvsA.AffymetrixCelFile append.AffymetrixCelSet
  append.CnagCfhSet applyAnyOrder
  applyAnyOrder.CopyNumberChromosomalModel applyCCF0
  applyCCF0.CopyNumberChromosomalModel applyCFC0
  applyCFC0.CopyNumberChromosomalModel applyToUnitIntensities
  applyToUnitIntensities.AffymetrixCelSet AromaAffymetrix AromaUfcFile
  AromaUflFile as.AffymetrixCelSet 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.ChipTypeReporter as.character.ChromosomalModel
  as.character.ChromosomeExplorer as.character.CnagCfhFile
  as.character.CopyNumberChromosomalModel as.character.DChipDcpFile
  as.character.DChipQuantileNormalization as.character.Explorer
  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.Transform
  as.character.TransformReport as.character.WeightsFile
  as.character.WeightsSet as.CnagCfhSet as.DChipDcpSet bgAdjustGcrma
  bgAdjustOptical bgAdjustRma boxplotStats boxplotStats.ChipEffectSet
  byChipType.AffymetrixCsvGenomeInformation
  byChipType.AffymetrixProbeTabFile byChipType.AffymetrixTabularFile
  byChipType.AffymetrixTsvFile byChipType.AromaUnitTabularBinaryFile
  byChipType.UflSnpInformation byName.AffymetrixCelSet
  byName.CnagCfhSet byName.DChipDcpSet
  byPath.AffymetrixCelSetTuple calcRawCnStats
  calcRawCnStats.CopyNumberChromosomalModel calcRawCnStats.default
  calculateAverages
  calculateAverages.FragmentEquivalentClassNormalization
  calculateBaseline calculateChromosomeStatistics
  calculateChromosomeStatistics.CopyNumberChromosomalModel
  calculateFieldBoxplotStats calculateFieldBoxplotStats.ChipEffectSet
  calculateMargins calculateMargins.ChipTypeReporter
  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 cdfMergeGroups cdfMergeStrands
  ChipEffectSetTuple clearCache.AffymetrixCdfFile
  clearCache.AffymetrixCelFile clearCache.AffymetrixCelSet
  clearCache.AffymetrixCelSetTuple clearCache.AffymetrixCnChpFile
  clearCache.AffymetrixNetAffxCsvFile clearCache.AffymetrixProbeTabFile
  clearCache.AffymetrixTsvFile clearCache.AllelicCrosstalkCalibration
  clearCache.ChipEffectFile clearCache.ChipEffectSet
  clearCache.ChromosomalModel clearCache.CnagCfhFile
  clearCache.CnagCfhSet clearCache.CopyNumberChromosomalModel
  clearCache.ExonChipEffectFile clearCache.FirmaFile
  clearCache.FirmaModel clearCache.FirmaSet
  clearCache.FragmentEquivalentClassNormalization
  clearCache.FragmentLengthNormalization clearCache.GenomeInformation
  clearCache.ParameterCelFile clearCache.ProbeAffinityFile
  clearCache.ProbeLevelModel clearCache.QualityAssessmentFile
  clearCache.QuantileNormalization clearCache.ResidualFile
  clearCache.ResidualSet clearCache.SmoothMultiarrayModel
  clearCache.SnpChipEffectFile clearCache.SnpInformation
  clearCache.Transform clearCache.TransformReport
  clearCache.UgpGenomeInformation clearCache.WeightsFile
  clearCache.WeightsSet clearData clone.AffymetrixCelFile
  clone.AffymetrixCelSet clone.AffymetrixCnChpFile clone.CnagCfhFile
  clone.CnagCfhSet compare computeAffinities convert convertUnits
  createBlankSet createBlankSet.AffymetrixCelSet createFrom
  createMonoCell createMonocellCdf createOutputTuple
  createOutputTuple.SmoothMultiarrayModel createParamCdf
  createParamCdf.ChipEffectFile createParamCdf.FirmaFile decode
  decode.ParameterCelFile dim.DChipDcpFile display.ChromosomeExplorer
  doCRMA doCRMA.default drawCnRegions drawCnRegions.DNAcopy
  drawCnRegions.profileCGH  drawCytoband.ChromosomalModel
  drawExtraAnnotations
  drawExtraAnnotations.default drawExtraAnnotations.profileCGH encode
  encode.ParameterCelFile estimateSds excludeChrXFromFit
  excludeChrXFromFit.DChipQuantileNormalization extractAffyBatch
  extractCopyNumberOutliers extractCopyNumberOutliers.DNAcopy
  extractCopyNumberOutliers.profileCGH extractCopyNumberRegions.DNAcopy
  extractCopyNumberRegions.profileCGH extractCopyNumberRegions.SCPfit
  extractDataFrame extractDataFrame.ParameterCelFile
  extractMatrix.ChipEffectFile extractMatrix.ChipEffectSet
  extractMatrix.FirmaFile extractMatrix.FirmaSet
  extractMatrix.ParameterCelFile
  extractRawCopyNumbers.CopyNumberChromosomalModel
  extractRawCopyNumbers.DNAcopy extractRawCopyNumbers.profileCGH
  extractRawCopyNumbers.SCPfit extractTheta extractTheta.ChipEffectFile
  extractTheta.ChipEffectSet extractTheta.CnChipEffectFile
  extractTheta.CnChipEffectSet extractTheta.SnpChipEffectFile
  extractTheta.SnpChipEffectSet extractTotalAndFreqB
  extractTotalAndFreqB.CnChipEffecSet
  extractTotalAndFreqB.CnChipEffectFile
  extractTotalAndFreqB.SnpChipEffectFile
  extractTotalAndFreqB.SnpChipEffectSet findByCdf2 findByCdf2.default
  findByChipType.AffymetrixCsvFile
  findByChipType.AffymetrixCsvGenomeInformation
  findByChipType.AffymetrixNetAffxCsvFile
  findByChipType.AffymetrixProbeTabFile
  findByChipType.AffymetrixTabularFile findByChipType.AffymetrixTsvFile
  findByChipType.DChipGenomeInformation
  findByChipType.DChipSnpInformation findByChipType.UflSnpInformation
  findByChipType.UgpGenomeInformation findByName.AffymetrixCelSet
  findByName.ChipEffectSet findByName.CnagCfhSet findByName.DChipDcpSet
  findUnitsTodo findUnitsTodo.ChipEffectFile
  findUnitsTodo.ChipEffectSet findUnitsTodo.ExonChipEffectSet
  findUnitsTodo.FirmaFile findUnitsTodo.FirmaSet
  findUnitsTodo.QualityAssessmentFile findUnitsTodo.ResidualFile
  findUnitsTodo.ResidualSet findUnitsTodo.WeightsFile
  findUnitsTodo.WeightsSet fit fit.ChromosomalModel fitGlad
  fitGlad.CnChipEffectSet  fitOneChromosome
  fitOneChromosome.SmoothMultiarrayModel fitPlasqUnit
  fitPlasqUnit.matrix fitQuantileNormFcn fixSearchPath
  fixSearchPath.AromaAffymetrix fromCdf fromCdf.AffymetrixProbeTabFile
  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.DChipDcpFile fromFiles.AffymetrixCelSet
  fromFiles.ChipEffectSet fromFiles.CnagCfhSet
  fromFiles.CnChipEffectSet fromFiles.DChipDcpSet
  fromFiles.ExonChipEffectSet fromFiles.FirmaSet fromFiles.ResidualSet
  fromFiles.SnpChipEffectSet fromFiles.WeightsSet fromName
  fromName.AffymetrixCelSet fromName.CnagCfhSet fromName.DChipDcpSet
  getAlias.ArrayExplorer getAlias.ChromosomalModel
  getAlias.TransformReport getAllelePairs getAllelePairUnitSets
  getAlleleProbePairs getAlleleProbePairs2
  getAlleleProbePairs2.AffymetrixCdfFile getAm getAM
  getAm.AffymetrixCelFile getAromaUfcFile
  getAromaUfcFile.FragmentEquivalentClassNormalization getAromaUflFile
  getAromaUflFile.UflSnpInformation
  getAromaUgpFile.UgpGenomeInformation getArrayNames
  getArrayNames.AffymetrixAptSummaryFile getArraysOfInput
  getArraysOfInput.ArrayExplorer getArraysOfInput.ChromosomeExplorer
  getAsFullCelFile getAsFullCelFile.ChipEffectFile getAsFullCelSet
  getAsFullCelSet.ChipEffectSet getAsteriskTags.AffineCnPlm
  getAsteriskTags.AffinePlm getAsteriskTags.AffineSnpPlm
  getAsteriskTags.AlleleSummation
  getAsteriskTags.AllelicCrosstalkCalibration
  getAsteriskTags.ArrayExplorer getAsteriskTags.AvgCnPlm
  getAsteriskTags.AvgPlm getAsteriskTags.AvgSnpPlm
  getAsteriskTags.CbsModel getAsteriskTags.ChromosomalModel
  getAsteriskTags.ExonRmaPlm getAsteriskTags.Explorer
  getAsteriskTags.FirmaModel
  getAsteriskTags.FragmentEquivalentClassNormalization
  getAsteriskTags.FragmentLengthNormalization
  getAsteriskTags.GenericReporter getAsteriskTags.GladModel
  getAsteriskTags.HetLogAddCnPlm getAsteriskTags.HetLogAddPlm
  getAsteriskTags.HetLogAddSnpPlm getAsteriskTags.MbeiCnPlm
  getAsteriskTags.MbeiPlm getAsteriskTags.MbeiSnpPlm
  getAsteriskTags.Model getAsteriskTags.ProbeLevelModel
  getAsteriskTags.QualityAssessmentModel
  getAsteriskTags.RawCopyNumberModel getAsteriskTags.RmaCnPlm
  getAsteriskTags.RmaPlm getAsteriskTags.RmaSnpPlm
  getAsteriskTags.ScaleNormalization getAsteriskTags.ScpModel
  getAsteriskTags.SmoothMultiarrayModel getAsteriskTags.SmoothRmaModel
  getAsteriskTags.SmoothSaModel getAsteriskTags.SnpChipEffectGroupMerge
  getAsteriskTags.Transform getAverage getAverage.AffymetrixCelSet
  getAverage.CnagCfhSet getAverageAsinh
  getAverageAsinh.AffymetrixCelSet getAverageAsinh.CnagCfhSet
  getAverageFile 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
  getCdf getCdf.AffymetrixChipTypeReporter getCdf.AffymetrixCnChpFile
  getCdf.AffymetrixProbeTabFile getCdf.AffymetrixTsvFile
  getCdf.AromaUnitTabularBinaryFile getCdf.ChipEffectGroupMerge
  getCdf.FirmaModel getCdf.FragmentEquivalentClassNormalization
  getCdf.FragmentLengthNormalization getCdf.GcContentNormalization
  getCdf.QualityAssessmentModel getCdf.TransformReport getCellIndices
  getCellIndices.ChipEffectFile getCellIndices.ChipEffectSet
  getCellIndices.CnChipEffectFile getCellIndices.CnPlm
  getCellIndices.CnProbeAffinityFile getCellIndices.ExonChipEffectFile
  getCellIndices.ExonProbeAffinityFile getCellIndices.ExonRmaPlm
  getCellIndices.FirmaFile getCellIndices.FirmaSet
  getCellIndices.ProbeAffinityFile getCellIndices.ProbeLevelModel
  getCellIndices.ResidualFile getCellIndices.ResidualSet
  getCellIndices.SnpChipEffectFile getCellIndices.SnpPlm
  getCellIndices.SnpProbeAffinityFile getCellIndices.WeightsFile
  getCellIndices.WeightsSet getCellMap getCellMap.FirmaFile
  getCellMap.ResidualFile getCellMap.WeightsFile getCellMapForMainCdf
  getCellMapForMainCdf.ChipEffectFile getChipEffectFileClass
  getChipEffectFileClass.ChipEffectSet
  getChipEffectFileClass.CnChipEffectSet
  getChipEffectFileClass.ExonChipEffectSet
  getChipEffectFileClass.SnpChipEffectSet getChipEffectFiles
  getChipEffectFiles.ChromosomalModel 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.AffymetrixChipTypeReporter
  getChipType.AffymetrixCnChpFile getChipType.AffymetrixProbeTabFile
  getChipType.AffymetrixTsvFile getChipType.AromaChipTypeAnnotationFile
  getChipType.UflSnpInformation getChipType.UgpGenomeInformation
  getChipTypes.ChromosomalModel getChromosomes.GenomeInformation
  getChromosomes.UgpGenomeInformation getChromosomeStats
  getChromosomeStats.GenomeInformation getCnNames getColorMaps
  getColorMaps.ArrayExplorer getColorMaps.ChipTypeReporter
  getColorMaps.SpatialReporter getColumnNames.AromaUfcFile
  getColumnNames.AromaUflFile getCombineAlleles
  getCombineAlleles.CnChipEffectSet 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 getDimension
  getDimension.AffymetrixCdfFile getExclCells
  getExclCells.DChipQuantileNormalization
  getExclCells.QuantileNormalization getExcludes
  getExcludes.DChipDcpFile getExclusiveUnitSubsets
  getExclusiveUnitSubsets.FragmentEquivalentClassNormalization
  getExpandedCellMap getExpandedCellMap.ChipEffectFile
  getExpandedCellMap.CnChipEffectFile
  getExpandedCellMap.SnpChipEffectFile getField
  getField.AffymetrixTsvFile getFields.SnpInformation
  getFields.UflSnpInformation getFileClass.FirmaSet getFileFormat
  getFileFormat.AffymetrixCdfFile getFileFormat.AffymetrixCelFile
  getFileFormat.AffymetrixCnChpFile getFileFormat.DChipDcpFile
  getFilenameExtension.AromaUfcFile getFilenameExtension.AromaUflFile
  getFileSet getFileSet.AffymetrixFileSetReporter getFileSetClass
  getFileSetClass.FirmaModel getFirmaScores getFirmaSet
  getFirstCellIndices getFirstCellIndices.AffymetrixCdfFile
  getFirstCellPerUnitIndices
  getFirstCellPerUnitIndices.ExonChipEffectSet 
  getFitUnitFunction
  getFitUnitFunction.CnPlm getFitUnitFunction.FirmaModel
  getFitUnitFunction.ProbeLevelModel getFitUnitFunction.UnitModel
  getFragmentLengths getFragmentLengths.AffymetrixTsvFile
  getFragmentLengths.SnpInformation
  getFragmentLengths.UflSnpInformation getFragmentStarts
  getFragmentStarts.SnpInformation getFragmentStarts.UflSnpInformation
  getFragmentStops getFragmentStops.SnpInformation
  getFragmentStops.UflSnpInformation getFullName.AffymetrixCelSet
  getFullName.ChromosomalModel getFullName.CnagCfhSet
  getFullName.DChipDcpSet getFullName.Explorer
  getFullName.GenericReporter getFullName.QualityAssessmentModel
  getFullNames.ChipEffectSetTuple getFullNames.ChromosomalModel
  getFullNames.ChromosomeExplorer getGc getGc.AffymetrixTsvFile
  getGenome getGenome.ChromosomalModel getGenomeData
  getGenomeData.ChromosomalModel getGenomeFile
  getGenomeFile.ChromosomalModel getGenomeInformation
  getGroupDirections getGroupDirections.AffymetrixCdfFile
  getHeader.AffymetrixCnChpFile getHeader.DChipDcpFile getHeaderLength
  getHeaderLength.CnagCfhFile getHeaderV3 getHeaderV3.AffymetrixCelFile
  getIdentifier getIdentifier.AffymetrixCelFile
  getIdentifier.AffymetrixCelSet getIdentifier.AffymetrixFileSet
  getIdentifier.CnagCfhFile getIdentifier.CnagCfhSet
  getImage.AffymetrixCdfFile getImage.AffymetrixChipTypeReporter
  getImage.AromaUnitTabularBinaryFile getImage.ResidualFile
  getImage.WeightsFile getIncludePath getIncludePath.Explorer
  getIndexToRowMap getIndexToRowMap.AffymetrixProbeTabFile
  getInputDataSet getInputName getInputName.AffymetrixChipTypeReporter
  getInputName.AffymetrixFileSetReporter getInputName.GenericReporter
  getInputTags getInputTags.AffymetrixChipTypeReporter
  getInputTags.AffymetrixFileSetReporter getInputTags.GenericReporter
  getIntensities getLabel.Model getListOfCdfs
  getListOfCdfs.AffymetrixCelSetTuple getListOfCdfs.ArrayExplorer
  getListOfCdfs.ChromosomalModel getListOfChipEffects
  getListOfChipEffects.ChromosomalModel getListOfChipEffectSets
  getListOfChipEffectSets.ChromosomalModel getListOfGenomeInformations
  getListOfGenomeInformations.ChromosomalModel getListOfReporters
  getListOfReporters.ArrayExplorer getLog2Ratios
  getLog2Ratios.CopyNumberSegmentationModel getMainCdf
  getMainCdf.AffymetrixCdfFile getMainPath
  getMainPath.AffymetrixChipTypeReporter getMainPath.Explorer
  getMainPath.GenericReporter getMatrixChipEffectFiles
  getMatrixChipEffectFiles.CopyNumberChromosomalModel getMergeFunction
  getMergeFunction.ChipEffectGroupMerge
  getMergeFunction.SnpChipEffectGroupMerge getMergeGroups
  getMergeGroups.ExonChipEffectSet getMergeStrands
  getMergeStrands.SnpChipEffectSet getModel getMonoCell
  getMonoCell.AffymetrixCdfFile getMonocellCdf
  getMonocellCdf.AffymetrixCdfFile getName.AffymetrixPlatform
  getName.ChromosomalModel getName.FirmaModel
  getName.QualityAssessmentModel getNameOfInput
  getNameOfInput.ArrayExplorer getNameOfInput.ChromosomeExplorer
  getNameOfInput.Explorer getNames.ChromosomalModel
  getNames.ChromosomeExplorer getNormalizedIntensities
  getNormalizedIntensities.DChipDcpFile getOrderedFragmentPairMap
  getOrderedFragmentPairMap.AromaUfcFile getOrderedFragmentPairs
  getOrderedFragmentPairs.AromaUfcFile getOutputDataSet
  getOutputDataSet.ChipEffectTransform
  getOutputDataSet.FragmentEquivalentClassNormalization
  getOutputDataSet.FragmentLengthNormalization
  getOutputDataSet.GcContentNormalization getOutputFiles
  getOutputFiles.Transform getOutputIdentifier
  getOutputIdentifier.QuantileNormalization getOutputTuple
  getOutputTuple.SmoothMultiarrayModel getPackageName
  getParameter.AffymetrixAptSummaryFile
  getParameters.AllelicCrosstalkCalibration
  getParameters.BackgroundCorrection getParameters.ChipEffectFile
  getParameters.ChipEffectGroupMerge getParameters.ChipEffectSet
  getParameters.CnChipEffectFile
  getParameters.DChipQuantileNormalization
  getParameters.ExonChipEffectFile
  getParameters.FragmentEquivalentClassNormalization
  getParameters.FragmentLengthNormalization
  getParameters.GcContentNormalization
  getParameters.GcRmaBackgroundCorrection getParameters.Model
  getParameters.OpticalBackgroundCorrection
  getParameters.ParameterCelFile getParameters.ProbeAffinityFile
  getParameters.QuantileNormalization getParameters.ResidualFile
  getParameters.ResidualSet getParameters.RmaBackgroundCorrection
  getParameters.ScaleNormalization getParameters.SnpChipEffectFile
  getParameters.SnpChipEffectGroupMerge
  getParameters.SpatialRowColumnNormalization getParameters.Transform
  getParameters.WeightsFile getParameters.WeightsSet
  getParametersAsString getParametersAsString.ChipEffectFile
  getParametersAsString.ChipEffectSet getParametersAsString.Model
  getParametersAsString.ProbeAffinityFile
  getParametersAsString.ResidualFile getParametersAsString.ResidualSet
  getParametersAsString.Transform getParametersAsString.WeightsFile
  getParametersAsString.WeightsSet getParameterSet
  getParameterSet.AvgPlm getParameterSet.CnPlm getParameterSet.Model
  getParameterSet.ProbeLevelModel getParameterSet.RmaPlm
  getParameterSet.SnpPlm getParentPath getParentPath.ChromosomalModel
  getPath.AffymetrixCelSetReporter getPath.AffymetrixChipTypeReporter
  getPath.ChromosomalModel getPath.ChromosomeExplorer getPath.Explorer
  getPath.GenericReporter getPath.QualityAssessmentModel getPcuTheta
  getPcuTheta.ChromosomalModel getPlasqTypes
  getPlatform.AffymetrixCdfFile getPlatform.AffymetrixCelFile
  getPlatform.AromaChipTypeAnnotationFile getPlm getPlm.FirmaModel
  getPlm.QualityAssessmentModel getPosition.AffymetrixTsvFile
  getPositionChipTypeUnit getPositionChipTypeUnit.ChromosomalModel
  getPositionChipTypeUnit.CopyNumberSegmentationModel getPositions
  getProbeAffinities getProbeAffinities.ExonRmaPlm getProbeAffinityFile
  getProbeAffinityFile.AffinePlm getProbeAffinityFile.AvgPlm
  getProbeAffinityFile.CnPlm getProbeAffinityFile.ExonRmaPlm
  getProbeAffinityFile.MbeiPlm getProbeAffinityFile.RmaPlm
  getProbeAffinityFile.SnpPlm getProbesetIds
  getProbesetIds.AffymetrixAptSummaryFile getQuantificationScale
  getQuantificationScale.AffymetrixAptSummaryFile getRawCnData
  getRawCnData.CopyNumberChromosomalModel getRawData
  getRawData.AffymetrixCnChpFile getRawIntensities
  getRawIntensities.DChipDcpFile
  getReadArguments.AffymetrixAptSummaryFile getRectangle
  getRectangle.AffymetrixCelFile getReference
  getReference.ChipTypeReporter getReference.SpatialReporter
  getReferenceSetTuple getReferenceSetTuple.CopyNumberChromosomalModel
  getRefSetTuple getRefSetTuple.CopyNumberChromosomalModel getRegions
  getRegions.CopyNumberSegmentationModel getRegions.profileCGH
  getReportPath getReportPath.ChromosomalModel getReportPathPattern
  getReportPathPattern.Explorer getReportSet
  getReportSet.ChipTypeReporter getReportSet.GenericReporter
  getReportSet.SpatialReporter getResidualFileClass
  getResidualFileClass.ResidualSet getResiduals getResidualSet
  getResidualSet.ProbeLevelModel getResidualSetClass
  getResidualSetClass.ProbeLevelModel getRestructor
  getRestructor.AffymetrixCdfFile getRootPath
  getRootPath.AlleleSummation getRootPath.ChipEffectTransform
  getRootPath.ChromosomalModel getRootPath.Explorer
  getRootPath.FirmaModel getRootPath.GenericReporter
  getRootPath.ProbeLevelModel getRootPath.ProbeLevelTransform
  getRootPath.QualityAssessmentModel getRootPath.SmoothMultiarrayModel
  getRootPath.SmoothRmaModel getRootPath.Transform
  getRootPath.TransformReport getSampleLayerName
  getSampleLayerName.Explorer getSampleLayerPrefix
  getSampleLayerPrefix.Explorer getSetTag getSetTag.ChromosomalModel
  getSetTag.RawCopyNumberModel getSetTuple getSetTuple.ArrayExplorer
  getSetTuple.ChromosomalModel getSetTuple.ChromosomeExplorer
  getSnpInformation getSnpInformation.AffymetrixCdfFile getSnpNames
  getSpar getSpar.SpatialRowColumnNormalization getSubname
  getSubname.Explorer getSubsetToAvg
  getSubsetToAvg.AllelicCrosstalkCalibration
  getSubsetToAvg.QuantileNormalization
  getSubsetToAvg.ScaleNormalization getSubsetToFit
  getSubsetToFit.FragmentEquivalentClassNormalization
  getSubsetToFit.FragmentLengthNormalization
  getSubsetToFit.GcContentNormalization getSubsetToUpdate
  getSubsetToUpdate.BackgroundCorrection
  getSubsetToUpdate.DChipQuantileNormalization
  getSubsetToUpdate.QuantileNormalization
  getSubsetToUpdate.ScaleNormalization getTags.ChromosomalModel
  getTags.CopyNumberSegmentationModel getTags.FirmaModel
  getTags.QualityAssessmentModel getTagsOfInput
  getTagsOfInput.ArrayExplorer getTagsOfInput.ChromosomeExplorer
  getTagsOfInput.Explorer getTargetAverages
  getTargetAverages.FragmentEquivalentClassNormalization
  getTargetDistribution getTargetDistribution.QuantileNormalization
  getTargetDistributionIdentifier
  getTargetDistributionIdentifier.QuantileNormalization
  getTargetDistributionPathname
  getTargetDistributionPathname.QuantileNormalization getTargetFunction
  getTargetFunction.FragmentLengthNormalization
  getTargetFunction.GcContentNormalization getTargetFunctions
  getTargetFunctions.FragmentLengthNormalization getTemplatePath
  getTemplatePath.Explorer getThetas getThetas.DChipDcpFile getThetasAB
  getThetasAB.DChipDcpFile getThetaStds getThetaStds.DChipDcpFile
  getTimestamp getTimeStamp getTimeStamp.AffymetrixAptSummaryFile
  getTimestamp.AffymetrixCnChpFile getTimestamp.CnagCfhFile
  getTimestamps getTimestamps.AffymetrixCelSet getTimestamps.CnagCfhSet
  getUnitGroupCellChromosomePositionMap
  getUnitGroupCellChromosomePositionMap.AffymetrixCdfFile
  getUnitGroupCellChromosomePositionMap.ChipEffectFile
  getUnitGroupCellMap getUnitGroupCellMap.AffymetrixCdfFile
  getUnitGroupCellMap.AffymetrixCelSet getUnitGroupCellMap.FirmaFile
  getUnitGroupCellMap.ResidualFile getUnitGroupCellMap.WeightsFile
  getUnitGroupCellMapWithMonocell
  getUnitGroupCellMapWithMonocell.AffymetrixCdfFile
  getUnitGroupNamesFromUgcMap
  getUnitGroupNamesFromUgcMap.AffymetrixCdfFile getUnitIndices
  getUnitIntensities getUnitNames.AffymetrixNetAffxCsvFile
  getUnitNamesFile.AffymetrixCdfFile getUnitNamesFile.AffymetrixCelFile
  getUnitNamesFile.AffymetrixCelSet
  getUnitNamesFile.AffymetrixCnChpFile
  getUnitNamesFile.AffymetrixPlatform 
  getUnitNamesFile.TransformReport getUnitReadMap
  getUnitReadMap.AffymetrixCnChpFile getUnitSizes getUnitsOnChromosome
  getUnitsOnChromosome.GenomeInformation
  getUnitsOnChromosomes  getUnitsOnChromosomes.GenomeInformation
  getUnitsOnChromosome.UgpGenomeInformation getUnitTypes
  getWeights getWeightsFileClass
  getWeightsFileClass.WeightsSet getWeightsSet
  getWeightsSet.ProbeLevelModel getWeightsSetClass
  getWeightsSetClass.ProbeLevelModel getXAM getYY getYY.TransformReport
  hasMbeiData hasMbeiData.DChipDcpFile hasNormalizedData
  hasNormalizedData.DChipDcpFile hasUnitReadMap
  hasUnitReadMap.AffymetrixCnChpFile hasUnitTypes
  hasUnitTypes.AffymetrixCdfFile highlight highlight.AffymetrixCelFile
  identifyCells identifyCells.AffymetrixCdfFile image270 importFrom
  importFrom.AromaUnitTabularBinaryFile
  importFromAffymetrixNetAffxCsvFile
  importFromAffymetrixNetAffxCsvFile.AromaUflFile
  importFromAffymetrixNetAffxCsvFile.AromaUgpFile
  importFromAffymetrixNetAffxCsvFile.AromaUnitTabularBinaryFile
  importFromAffymetrixTabularFile
  importFromAffymetrixTabularFile.AromaUfcFile
  importFromAffymetrixTabularFile.AromaUgpFile
  importFromAffymetrixTabularFile.AromaUnitTabularBinaryFile
  importFromApt importFromDChip importFromDChipGenomeInformation
  importFromDChipGenomeInformation.AromaUnitTabularBinaryFile
  importFromGenericTabularFile.AromaUnitTabularBinaryFile
  importFromGenomeInformation importFromGenomeInformation.AromaUgpFile
  importFromGenomeInformation.AromaUnitTabularBinaryFile
  inferParameters inferParameters.CnChipEffectSet
  inferParameters.SnpChipEffectSet isCompatibleWithCdf
  isCompatibleWithCdf.GenomeInformation
  isCompatibleWithCdf.SnpInformation
  isCompatibleWithCdf.UflSnpInformation
  isCompatibleWithCdf.UgpGenomeInformation isDuplicated isMonocellCdf
  isMonocellCdf.AffymetrixCdfFile isPaired
  isPaired.CopyNumberChromosomalModel isPm isSnpChip isUnitGroupCellMap
  isUnitGroupCellMap.data.frame isUnitGroupCellMap.default
  isUnitGroupCellMap.matrix mergeGroups mergeGroups.ChipEffectFile
  mergeStrands mergeStrands.CnChipEffectFile
  mergeStrands.SnpChipEffectFile migrateTool
  migrateTool.CopyNumberSegmentationModel
  nbrOfArrays.AffymetrixAptSummaryFile
  nbrOfArrays.AffymetrixCelSetReporter
  nbrOfArrays.QualityAssessmentModel nbrOfArrays.TransformReport
  nbrOfCells nbrOfCells.AffymetrixCdfFile nbrOfCells.AffymetrixCelFile
  nbrOfCells.CnagCfhFile nbrOfCells.DChipDcpFile
  nbrOfChipTypes.ArrayExplorer nbrOfColumns.AffymetrixCdfFile
  nbrOfEnzymes nbrOfEnzymes.AromaUfcFile nbrOfEnzymes.AromaUflFile
  nbrOfEnzymes.SnpInformation nbrOfEnzymes.UflSnpInformation
  nbrOfQcUnits nbrOfQcUnits.AffymetrixCdfFile
  nbrOfRows.AffymetrixCdfFile nbrOfSnps nbrOfSnps.CnagCfhFile
  nbrOfUnits.AffymetrixCdfFile nbrOfUnits.DChipDcpFile
  nbrOfUnits.GenomeInformation nbrOfUnits.SnpInformation
  nbrOfUnits.UflSnpInformation nbrOfUnits.UgpGenomeInformation newPlot
  newPlot.CopyNumberChromosomalModel normalizeOneArrayVector
  normalizeOneArrayVector.FragmentEquivalentClassNormalization
  onFitAddGenotypeCalls onFitAddGenotypeCalls.default
  onFitAddGenotypeCalls.GladModel patch patch.AromaAffymetrix
  plasqGaussian plot.CopyNumberSegmentationModel plot.profileCGH
  plotAxesLayers plotAxesLayers.CopyNumberChromosomalModel plotBasepair
  plotBasepair.AllelicCrosstalkCalibration plotBoxplot
  plotBoxplot.ChipEffectSet plotBoxplotStats plotChromosomesLayers
  plotChromosomesLayers.CopyNumberChromosomalModel
  plotCopyNumberRegionLayers
  plotCopyNumberRegionLayers.CopyNumberSegmentationModel
  plotCytobandLayers plotCytobandLayers.CopyNumberChromosomalModel
  plotFitLayers plotFitLayers.CopyNumberChromosomalModel
  plotGridHorizontalLayers
  plotGridHorizontalLayers.CopyNumberChromosomalModel plotImage
  plotMargins plotMargins.ChipTypeReporter plotMargins.SpatialReporter
  plotMvsX plotNuse plotNuse.QualityAssessmentModel plotProfile2
  plotProfile2.profileCGH plotRawCNs plotRawCNs.profileCGH
  plotRawCopyNumbers plotRawCopyNumbers.CopyNumberChromosomalModel
  plotRle plotRle.QualityAssessmentModel plotSampleLayers
  plotSampleLayers.CopyNumberChromosomalModel
  plotXYCurve.TransformReport plotXYCurveLog2
  plotXYCurveLog2.TransformReport pointsRawCNs pointsRawCNs.default
  pointsRawCNs.profileCGH process process.AlleleSummation
  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 readCdfFields
  readCdfFields.AffymetrixChipTypeReporter readCdfGroupStrands
  readCdfRectangle readCdfRectangle.AffymetrixChipTypeReporter
  readCfhHeader readCfhHeader.default readCfhUnits readCfhUnits.default
  readCfnHeader readCfnHeader.default readCfnUnits readCfnUnits.default
  readData.AffymetrixTsvFile readData.GenomeInformation
  readData.SnpInformation readDataFrame.AffymetrixCdfFile
  readDataFrame.AffymetrixCsvGenomeInformation
  readDataFrame.AffymetrixProbeTabFile readDataFrame.AffymetrixTsvFile
  readDataFrame.AromaUfcFile readDataFrame.AromaUflFile
  readDataFrame.DChipGenomeInformation
  readDataFrame.DChipSnpInformation readDataFrame.GenomeInformation
  readDataFrame.SnpInformation readDataFrame.UflSnpInformation
  readDataFrame.UgpGenomeInformation readDataUnitChromosomePosition
  readDataUnitChromosomePosition.AffymetrixNetAffxCsvFile
  readDataUnitFragmentLength
  readDataUnitFragmentLength.AffymetrixNetAffxCsvFile 
  readGenomeWideSNP
  readGenomeWideSNP.DChipGenomeInformation
  readHeader.AffymetrixAptSummaryFile readMouse430
  readMouse430.DChipGenomeInformation readMouse430KenHardwired
  readMouse430KenHardwired.DChipGenomeInformation readPlasqTypes
  readPlasqTypes.AffymetrixCdfFile readProbesetIds
  readProbesetIds.AffymetrixAptSummaryFile readRawData
  readRawDataRectangle readRawDataRectangle.AffymetrixCelFile
  readRawDataRectangle.ChipTypeReporter
  readRawDataRectangle.SpatialReporter 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
  rescale.AllelicCrosstalkCalibration rescaleByAll
  rescaleByAll.AllelicCrosstalkCalibration rescaleByGroups
  rescaleByGroups.AllelicCrosstalkCalibration restruct
  restruct.AffymetrixCdfFile seq.TransformReport setAlias.ArrayExplorer
  setAlias.ChromosomalModel setAlias.TransformReport setArrays
  setBandwidth setBandwidth.SmoothMultiarrayModel setCdf
  setCdf.AffymetrixCnChpFile setColorMaps setColorMaps.ArrayExplorer
  setColorMaps.ChipTypeReporter setColorMaps.SpatialReporter
  setCombineAlleles setCombineAlleles.CnChipEffectSet
  setCombineAlleles.CnPlm setCombineAlleles.CnProbeAffinityFile
  setCustomFindCdf setCytoband setCytoband.ChromosomeExplorer
  setDecodeFunction setDecodeFunction.ParameterCelFile
  setEncodeFunction setEncodeFunction.ParameterCelFile setGenome
  setGenome.ChromosomalModel setGenomeInformation
  setGenomeInformation.AffymetrixCdfFile setLabel.Model
  setMergeFunction setMergeFunction.ChipEffectGroupMerge setMergeGroups
  setMergeGroups.ExonChipEffectSet setMergeGroups.ExonProbeAffinityFile
  setMergeGroups.ExonRmaPlm setMergeStrands
  setMergeStrands.SnpChipEffectSet setMergeStrands.SnpPlm
  setMergeStrands.SnpProbeAffinityFile setReference
  setReference.ChipTypeReporter setReference.SpatialReporter
  setReportPathPattern setReportPathPattern.Explorer setRestructor
  setSnpInformation setSnpInformation.AffymetrixCdfFile setSubname
  setSubname.Explorer setTags.Transform setUnitReadMap
  setUnitReadMap.AffymetrixCnChpFile setup setup.ArrayExplorer
  setup.ChromosomeExplorer setup.Explorer setup.GenericReporter
  SmoothSaModel smoothScatterMvsA SpatialRowColumnNormalization
  splitByReportPathPattern splitByReportPathPattern.Explorer
  stextChipType.AffymetrixCdfFile summaryOfUnits
  summaryOfUnits.AromaUflFile transformAffine
  transformAffine.AffymetrixCelFile transformAffine.AffymetrixCelSet
  translateColumnNames.AffymetrixAptSummaryFile
  translateColumnNames.AffymetrixTabularFile UflSnpInformation
  update.AromaAffymetrix updateDataFlat updateDataFlat.ChipEffectFile
  updateDataFlat.FirmaFile updateDataFlat.ResidualFile
  updateDataFlat.WeightsFile updateOnChipTypeJS
  updateOnChipTypeJS.ArrayExplorer updateOnLoadJS
  updateOnLoadJS.ArrayExplorer updateSamplesFile updateUnits
  updateUnits.ChipEffectFile updateUnits.ChipEffectSet
  updateUnits.FirmaFile updateUnits.FirmaSet
  updateUnits.ParameterCelFile updateUnits.ProbeAffinityFile
  updateUnits.ResidualFile updateUnits.ResidualSet
  updateUnits.WeightsFile updateUnits.WeightsSet
  verify.AffymetrixCsvGenomeInformation verify.AffymetrixTsvFile
  verify.DChipGenomeInformation verify.DChipSnpInformation
  verify.UflSnpInformation verify.UgpGenomeInformation write
  writeAsFullCelFile writeAsFullCelFile.ChipEffectFile writeAxesLayers
  writeAxesLayers.ChromosomeExplorer writeCopyNumberRegionLayers
  writeCopyNumberRegionLayers.ChromosomeExplorer writeCytobandLayers
  writeCytobandLayers.ChromosomeExplorer writeGraphs
  writeGraphs.ChromosomeExplorer writeGridHorizontalLayers
  writeGridHorizontalLayers.ChromosomeExplorer writeImage
  writeImage.ResidualFile writeImage.WeightsFile writeImageCombined
  writeImageCombined.TransformReport writeImages
  writeImages.ChipTypeReporter writeImages.SpatialReporter
  writeImages.TransformReport writeRawCopyNumberLayers
  writeRawCopyNumberLayers.ChromosomeExplorer writeRegions
  writeRegions.ChromosomeExplorer
  writeRegions.CopyNumberSegmentationModel writeRegions.GladModel
  writeRegions.profileCGH writeWig writeWig.CnChipEffectSet
  Transform
  getParallelSafe getParallelSafe.Explorer getParameterSet.ExonRmaPlm
  setParallelSafe setParallelSafe.Explorer
  allocate.AromaProbeSequenceTextFile
  allocateFromCdf.AromaProbeSequenceTextFile AromaProbeSequenceTextFile
  byChipType.AromaProbeSequenceTextFile
  cleanupNewlines cleanupNewlines.AromaProbeSequenceTextFile
  clearCache.BaseCountNormalization countBases
  countBases.AromaProbeSequenceTextFile
  countBases.BaseCountNormalization exportAromaSignalBinaryFileList
  exportAromaSignalBinaryFileList.CnChipEffectFile
  exportAromaSignalBinaryFileList.SnpChipEffectFile
  exportAromaSignalBinarySetList
  exportAromaSignalBinarySetList.SnpChipEffectSet
  findByChipType.AromaProbeSequenceTextFile getAromaFreqBCnBinarySet
  getAromaFreqBCnBinarySet.SnpChipEffectSet getAromaSignalBinarySetList
  getAromaSignalBinarySetList.SnpChipEffectSet getAromaTotalCnBinarySet
  getAromaTotalCnBinarySet.SnpChipEffectSet
  getAsteriskTags.BaseCountNormalization
  getCdf.AromaProbeSequenceTextFile getCellsFromXY
  getCellsFromXY.AromaProbeSequenceTextFile
  getChipType.AromaProbeSequenceTextFile
  getColumnNames.AffymetrixProbeTabFile getDataFileOffset
  getDataFileOffset.AromaProbeSequenceTextFile getHeaderParameters
  getHeaderParameters.AromaProbeSequenceTextFile
  getParameters.BaseCountNormalization getPlatform.AffymetrixCelSet
  getPlatform.AromaProbeSequenceTextFile
  getSubsetToFit.BaseCountNormalization getTargetFile
  getTargetFile.BaseCountNormalization getUnitGroupCellMatrixMap
  getUnitGroupCellMatrixMap.ChipEffectFile
  hasColumnHeader.AffymetrixProbeTabFile
  importFrom.AromaProbeSequenceTextFile
  importFromAffymetrixProbeTabFile
  importFromAffymetrixProbeTabFile.AromaProbeSequenceTextFile
  inferMmFromPmSequences
  inferMmFromPmSequences.AromaProbeSequenceTextFile isMissing
  isMissing.AromaProbeSequenceTextFile
  nbrOfCells.AromaProbeSequenceTextFile
  nbrOfColumns.AromaProbeSequenceTextFile
  nbrOfRows.AromaProbeSequenceTextFile 
  readDataFrame2 readDataFrame2.AffymetrixProbeTabFile
  readRawSequenceMatrix
  readRawSequenceMatrix.AromaProbeSequenceTextFile readRawSequences
  readRawSequences.AromaProbeSequenceTextFile readSequenceMatrix
  readSequenceMatrix.AromaProbeSequenceTextFile readSequenceStrings
  readSequenceStrings.AromaProbeSequenceTextFile
  readTableHeader.AromaProbeSequenceTextFile seqMatrixToStrings
  seqMatrixToStrings.matrix seqRawMatrixToStrings
  seqRawMatrixToStrings.matrix
  translateColumnNames.AffymetrixProbeTabFile
  translateFullName.AffymetrixProbeTabFile updateRawSequences
  updateRawSequences.AromaProbeSequenceTextFile updateSequenceStrings
  updateSequenceStrings.AromaProbeSequenceTextFile
 extractMatrix.AffymetrixCelFile fromChipType getAromaCellSequenceFile
  getAromaCellSequenceFile.BaseCountNormalization
  update2.AffymetrixCelSet updateSampleAnnotationSet
  updateSampleAnnotationSet.AffymetrixCelSet
  getSubsetOfCellIndices getSubsetOfCellIndices.AffymetrixCdfFile
  getSubsetTo getSubsetTo.BaseCountNormalization
  getSubsetToUpdate.BaseCountNormalization
 clearCache.ProbeLevelTransform2
  fitOne.AbstractProbeSequenceNormalization
  fitOne.BaseCountNormalization
  getAromaCellSequenceFile.AbstractProbeSequenceNormalization
  getAsteriskTags.ProbeLevelTransform2 getDesignMatrix
  getDesignMatrix.BaseCountNormalization
  getParameters.ProbeLevelTransform2 getSubsetTo.ProbeLevelTransform2
  getSubsetToFit.ProbeLevelTransform2
  getSubsetToUpdate.ProbeLevelTransform2
  getTargetFile.AbstractProbeSequenceNormalization predictOne
  predictOne.AbstractProbeSequenceNormalization
  predictOne.BaseCountNormalization
  allocateFromCdf.AromaCellSequenceFile
  importFromAffymetrixProbeTabFile.AromaCellSequenceFile inferMmFromPm
  inferMmFromPm.AromaCellSequenceFile
  fitOne.BasePositionNormalization
  getAsteriskTags.BasePositionNormalization
  getDesignMatrix.BasePositionNormalization
  getParameters.BasePositionNormalization
  predictOne.BasePositionNormalization
 fitOne.ScaleNormalization2 getNormalizeSignalsOne
  getNormalizeSignalsOne.ScaleNormalization2
  getParameters.ScaleNormalization2 writeSignals
  writeSignals.ProbeLevelTransform2
  clearCache.ProbeLevelTransform3 fitOne.ScaleNormalization3
  fitOne.UnitTypeScaleNormalization
  getAsteriskTags.ProbeLevelTransform3 getCellsTo
  getCellsTo.ProbeLevelTransform3 getCellsToFit
  getCellsToFit.ProbeLevelTransform3 getCellsToInternal
  getCellsToInternal.ProbeLevelTransform3 getCellsToUpdate
  getCellsToUpdate.ProbeLevelTransform3
  getNormalizeSignalsOne.ScaleNormalization3
  getNormalizeSignalsOne.UnitTypeScaleNormalization
  getParameters.ProbeLevelTransform3 getParameters.ScaleNormalization3
  getParameters.UnitTypeScaleNormalization getSubsetOfCellIndices2
  getSubsetOfCellIndices2.AffymetrixCdfFile getSubsetOfUnits
  getSubsetOfUnits.AffymetrixCdfFile getUnitsTo
  getUnitsTo.ProbeLevelTransform2 getUnitsTo.ProbeLevelTransform3
  getUnitsToFit getUnitsToFit.ProbeLevelTransform3 getUnitsToUpdate
  getUnitsToUpdate.ProbeLevelTransform3 indexOfMissingSequences
  indexOfMissingSequences.AbstractProbeSequenceNormalization
  writeSignals.ProbeLevelTransform3
  getTotalAndFreqBSets.SnpChipEffectSet
getTotalAndFreqBSets
computeAffinities2
getParameters.AbstractProbeSequenceNormalization
  clearCache.ReseqCrosstalkCalibration
  getAsteriskTags.ReseqCrosstalkCalibration getCellQuartets
  getCellQuartets.AffymetrixCdfFile
  getParameters.AbstractProbeSequenceNormalization
  getParameters.ReseqCrosstalkCalibration
  getSubsetToAvg.ReseqCrosstalkCalibration isResequenceChip
  readUnitsByQuartets 
  rescaleByAll.ReseqCrosstalkCalibration
extractTheta.DChipDcpFile extractTheta.DChipDcpSet
  as.character.DChipCdfBinFile clearCache.DChipCdfBinFile
  fromFile.DChipCdfBinFile getCellDim getCellDim.DChipCdfBinFile
  getChipType.DChipCdfBinFile getFileFormat.DChipCdfBinFile
  getHeader.DChipCdfBinFile getPlatform.DChipCdfBinFile
  getUnitNames.DChipCdfBinFile getUnitSizes.DChipCdfBinFile
  nbrOfCells.DChipCdfBinFile nbrOfUnits.DChipCdfBinFile
  readDataFrame.DChipCdfBinFile
  as.AffymetrixCnChpSet as.character.DChipCdfBinFile
  byName.AffymetrixCnChpSet clearCache.DChipCdfBinFile extractLogRatios
  extractLogRatios.AffymetrixCnChpFile
  extractLogRatios.AffymetrixCnChpSet findByName.AffymetrixCnChpSet
  fromFile.DChipCdfBinFile fromFiles.AffymetrixCnChpSet
  getCdf.AffymetrixCnChpSet getCellDim getCellDim.DChipCdfBinFile
  getChipType.DChipCdfBinFile getFileFormat.DChipCdfBinFile
  getFullName.AffymetrixCnChpSet getHeader.DChipCdfBinFile
  getPlatform.DChipCdfBinFile getUnitNames.DChipCdfBinFile
  getUnitSizes.DChipCdfBinFile nbrOfCells.DChipCdfBinFile
  nbrOfUnits.DChipCdfBinFile readDataFrame.DChipCdfBinFile
  readRawData.AffymetrixCnChpFile setCdf.AffymetrixCnChpSet
calibrateOne calibrateOne.ReseqCrosstalkCalibration
fitOne.ReseqCrosstalkCalibration fitOneArray
fitOneArray.SingleArrayUnitModel getAlleleCellPairs
getAlleleProbePairs3 getAsteriskTags.UnitModel
getFitUnitFunction.MultiArrayUnitModel
getFitUnitFunction.SingleArrayUnitModel getFitUnitGroupFunction
getParameterSet.UnitModel getSetsOfProbes
getSetsOfProbes.AllelicCrosstalkCalibration
getSetsOfProbes.ReseqCrosstalkCalibration
fitCnProbes fitCnProbes.UnitModel
  getFitSingleCellUnitFunction getFitSingleCellUnitFunction.UnitModel
  nbrOfCellsPerUnit nbrOfCellsPerUnit.AffymetrixCdfFile
  nbrOfCellsPerUnitGroup nbrOfCellsPerUnitGroup.AffymetrixCdfFile
  nbrOfGroupsPerUnit 
  getFitUnitGroupFunction.SmoothMultiarrayModel
  getFitUnitGroupFunction.SmoothRmaModel
  getFitUnitGroupFunction.SmoothSaModel
  getFitFunction getFitFunction.MultiArrayUnitModel
  allocate.AromaCellMatchScoreFile
  allocateFromCdf.AromaCellMatchScoreFile AromaCellMatchScoreFile
  bpmapCluster2Cdf byChipType.AromaCellMatchScoreFile convertToUnique
  convertToUnique.AffymetrixCelSet createUnique createUniqueCdf
  fitOne.MatNormalization getAromaCellMatchScoreFile
  getAromaCellMatchScoreFile.MatNormalization
  getAsteriskTags.MatNormalization
  getColumnNames.AromaCellMatchScoreFile
  getDesignMatrix.MatNormalization
  getFilenameExtension.AromaCellMatchScoreFile
  getParameters.MatNormalization getUnique getUnique.AffymetrixCdfFile
  getUniqueCdf getUniqueCdf.AffymetrixCdfFile
  getUnitGroupCellMapWithUnique
  getUnitGroupCellMapWithUnique.AffymetrixCdfFile importFromBpMap
  importFromBpMap.AromaCellMatchScoreFile
  importFromBpMap.AromaCellSequenceFile
  isMissing.AromaCellMatchScoreFile isUniqueCdf
  isUniqueCdf.AffymetrixCdfFile predictOne.MatNormalization
  readMatchScores readMatchScores.AromaCellMatchScoreFile
  updateMatchScores updateMatchScores.AromaCellMatchScoreFile
  fitOne.LinearModelProbeSequenceNormalization getCrossProductXTX
  getCrossProductXTX.MatNormalization getNormalEquations
  getNormalEquations.LinearModelProbeSequenceNormalization
  getSignalTransform getSignalTransform.BasePositionNormalization
  getSignalTransform.LinearModelProbeSequenceNormalization
  predictOne.LinearModelProbeSequenceNormalization
getDesignMatrix.LinearModelProbeSequenceNormalization
   allocateFromCdf.AromaCellPositionFile
  extractTotalAndFreqB.CnChipEffectSet
  getListOfPriors
  getListOfPriors.MultiArrayUnitModel 
  plotAllelePairs plotAllelePairs.AllelicCrosstalkCalibration
  readPositions readPriorsByUnits
  readPriorsByUnits.MultiArrayUnitModel setListOfPriors
  setListOfPriors.MultiArrayUnitModel updatePositions
findUnitsTodo.AlleleSummation
getZooms getZooms.ChromosomeExplorer setZooms
  setZooms.ChromosomeExplorer
  drawCnRegions.HaarSeg extractCopyNumberRegions.HaarSeg
  extractRawCopyNumbers.HaarSeg 
  getAsteriskTags.HaarSegModel getFit getFit.BasePositionNormalization
getAromaCellPositionFile getAromaCellPositionFile.MatSmoothing
  getParameters.MatSmoothing isDone.MatSmoothing
  extractChromosomalDataFrame
  extractChromosomalDataFrame.ChipEffectFile
  extractChromosomalDataFrame.ChipEffectSet extractCNT
  extractCNT.SnpChipEffectFile extractCNT.SnpChipEffectSet
  getUnitGroupCellArrayMap getUnitGroupCellArrayMap.ChipEffectFile
  writeCNT writeCNT.SnpChipEffectFile writeCNT.SnpChipEffectSet
  validate.AvgPlm validate.MultiArrayUnitModel
  allocate.CrlmmParametersFile byName.CrlmmParametersSet CrlmmModel
  extractSnpCnvQSet
  extractSnpCnvQSet.SnpChipEffectSet extractSnpQSet
  extractSnpQSet.SnpChipEffectSet extractTheta.SnpCnvQSet
  extractTheta.SnpQSet findUnitsTodo.CrlmmModel
  findUnitsTodo.CrlmmParametersFile findUnitsTodo.CrlmmParametersSet
  fit.CrlmmModel fromFiles.CrlmmParametersSet
  getAsteriskTags.CrlmmModel getCallSet getCallSet.CrlmmModel
  getChipType.CrlmmModel getCrlmmParametersSet
  getCrlmmParametersSet.CrlmmModel getCrlmmPriors
  getCrlmmPriors.CrlmmModel getCrlmmSNPs getCrlmmSNPs.CrlmmModel
  getCrlmmSNPsOnChrX getCrlmmSNPsOnChrX.CrlmmModel
  getParameterSet.CrlmmModel getPlatformDesignDB
  getPlatformDesignDB.CrlmmModel getRootPath.CrlmmModel
  getUnitsToFit.CrlmmModel justSNPRMA justSNPRMA.AffymetrixCelSet
  justSNPRMA.character
 exportAromaSignalBinaryFileList.default
 exportAromaUnitSignalBinaryFileList
 exportAromaUnitSignalBinaryFileList.SnpChipEffectFile
 exportAromaUnitSignalBinarySetList
 exportAromaUnitSignalBinarySetList.default
 exportAromaUnitSignalBinarySetList.SnpChipEffectSet
 extractTotalAndFracB extractTotalAndFracB.SnpChipEffectFile
 extractTotalAndFreqB.default getAromaFracBCnBinarySet
 getAromaFracBCnBinarySet.SnpChipEffectSet
 getAromaFreqBCnBinarySet.default getAromaUnitSignalBinarySetList
 getAromaUnitSignalBinarySetList.SnpChipEffectSet getTotalAndFracBSets
 getTotalAndFracBSets.SnpChipEffectSet getTotalAndFreqBSets.default
 calculateConfidenceScores calculateConfidenceScores.CrlmmModel
 getConfidenceScoreSet getConfidenceScoreSet.CrlmmModel
 getCrlmmSplineParameters getCrlmmSplineParameters.CrlmmModel
 readParameter readParameter.CrlmmParametersFile updateParameter
 updateParameter.CrlmmParametersFile
Env2Cdf
PdInfo2Cdf
 getCombineAlleles.CnPlm getListOfAromaUgpFiles
 getListOfAromaUgpFiles.ChromosomalModel getListOfUnitNamesFiles
 getListOfUnitNamesFiles.AffymetrixCelSetTuple
 getListOfUnitNamesFiles.ArrayExplorer
 getListOfUnitNamesFiles.ChromosomalModel getMergeStrands.SnpPlm
 exportTotalAndFracB exportTotalAndFracB.SnpChipEffectFile
  exportTotalAndFracB.SnpChipEffectSet getAromaUnitFracBCnBinarySet
  getAromaUnitFracBCnBinarySet.default getAromaUnitTotalCnBinarySet
  getAromaUnitTotalCnBinarySet.default
 byChipType.DChipCdfBinFile exportTotalAndFracB.DChipDcpSet
 findByChipType.DChipCdfBinFile getCdfBin getCdfBin.DChipDcpSet
 getChipType.DChipDcpSet mapToUnitNamesFile
 mapToUnitNamesFile.DChipCdfBinFile
exportTotalCnRatioSet.AffymetrixCnChpSet  exportTotalCnRatioSet
 exportTotalAndFracB.CnChipEffectFile
  exportTotalAndFracB.CnChipEffectSet
 getDefaultSettings.AromaAffymetrix getDefaultSettings.Package
  getSettings getSettings.Package setSettings setSettings.Package
 updateSettings updateSettings.Package
getDefaultSettings
plotCovariateEffects.GcContentNormalization2
  allocateFromCdf.AromaUnitGcContentFile AromaUgcFile
  AromaUnitGcContentFile clearCache.AdditiveCovariatesNormalization
  getAsteriskTags.AdditiveCovariatesNormalization
  getCdf.AdditiveCovariatesNormalization
  getColumnNames.AromaUnitGcContentFile getCovariates
  getCovariates.AdditiveCovariatesNormalization
  getCovariates.GcContentNormalization2
  getFilenameExtension.AromaUnitGcContentFile getGcContent
  getGcContent.GcContentNormalization
  getOutputDataSet.AdditiveCovariatesNormalization
  getParameters.AdditiveCovariatesNormalization
  getSubsetToFit.AdditiveCovariatesNormalization
  getTargetFunctions.AdditiveCovariatesNormalization
  importFromAffymetrixNetAffxCsvFile.AromaUnitGcContentFile
  plotCovariateEffects writeSgr
  writeSgr.AffymetrixCelSet
getParameters.NormExpBgCorrection
  getAsteriskTags.LimmaBackgroundCorrection
  getAsteriskTags.NormExpBackgroundCorrection
  getParameters.LimmaBackgroundCorrection
  getParameters.NormExpBackgroundCorrection getSubsetToUpdate0
  getSubsetToUpdate0.LimmaBackgroundCorrection
 getOutputDataSet00 getOutputDataSet00.AdditiveCovariatesNormalization
 getOutputDataSet00.FragmentEquivalentClassNormalization
 getOutputDataSet00.FragmentLengthNormalization
 getOutputDataSet00.GcContentNormalization getOutputDataSetOLD20090509
 getOutputDataSetOLD20090509.Transform
 getProbeSequenceData getProbeSequenceData.AffymetrixCdfFile
 readSequenceDataFrame readSequenceDataFrame.AffymetrixProbeTabFile
 addBy addBy.RawGenomicSignals applyBinaryOperator
 applyBinaryOperator.RawGenomicSignals clearCache.TextUnitNamesFile
 divideBy divideBy.RawGenomicSignals extractRawAlleleBFractions
 extractRawAlleleBFractions.default getHeaderParameters
 getHeaderParameters.TextUnitNamesFile
 getUnitNamesFile.AromaPlatformInterface multiplyBy
 multiplyBy.RawGenomicSignals plot.RawAlleleBFractions subtractBy
 subtractBy.RawGenomicSignals
 getFitFunction.CbsModel getFitFunction.CopyNumberSegmentationModel
  getFitFunction.GladModel getFitFunction.HaarSegModel
fitOne getAsteriskTags.CopyNumberSegmentationModel
getExpectedOutputFiles.MatSmoothing
 getExpectedOutputFullnames.MatSmoothing
  getListOfUnitTypesFiles getListOfUnitTypesFiles.AffymetrixCelSetTuple
  getListOfUnitTypesFiles.ArrayExplorer
  getListOfUnitTypesFiles.ChromosomalModel
  getUnitTypesFile.AffymetrixCdfFile getUnitTypesFile.AffymetrixCelFile
  getUnitTypesFile.AffymetrixCelSet
  getUnitTypesFile.AffymetrixCnChpFile
  getUnitTypesFile.AffymetrixPlatform getUnitTypesFile.TransformReport
  getListOfUnitTypesFiles getListOfUnitTypesFiles.AffymetrixCelSetTuple
  getListOfUnitTypesFiles.ArrayExplorer
  getListOfUnitTypesFiles.ChromosomalModel
  getUnitTypesFile.AffymetrixCdfFile getUnitTypesFile.AffymetrixCelFile
  getUnitTypesFile.AffymetrixCelSet
  getUnitTypesFile.AffymetrixCnChpFile
  getUnitTypesFile.AffymetrixPlatform getUnitTypesFile.TransformReport
