Package: aroma.affymetrix 3.2.2
aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets
A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.
Authors:
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aroma.affymetrix/json (API)
NEWS
| # Install 'aroma.affymetrix' in R: |
| install.packages('aroma.affymetrix', repos = c('https://henrikbengtsson.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/henrikbengtsson/aroma.affymetrix/issues
affymetrixanalysiscopy-numberdnaexpressionhpclarge-scalemicroarraynotebookreproducibilityrna
Last updated 7 months agofrom:4e3d784440 (on master). Checks:OK: 1 NOTE: 5 WARNING: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 16 2024 |
| R-4.5-win | NOTE | Aug 16 2024 |
| R-4.5-linux | NOTE | Aug 16 2024 |
| R-4.4-win | WARNING | Aug 16 2024 |
| R-4.4-mac | NOTE | Aug 16 2024 |
| R-4.3-win | NOTE | Aug 16 2024 |
| R-4.3-mac | NOTE | Aug 16 2024 |
Exports:AbstractProbeSequenceNormalizationaddColorMapaddColorMap.ArrayExploreraddColorMap.SpatialReporteraddExclCellsaddExclCells.DChipQuantileNormalizationAdditiveCovariatesNormalizationAffineCnPlmAffinePlmAffineSnpPlmAffymetrixAptSummaryFileAffymetrixCdfFileAffymetrixCelFileAffymetrixCelSetAffymetrixCelSetReporterAffymetrixCelSetTupleAffymetrixCnChpFileAffymetrixCnChpSetAffymetrixCsvFileAffymetrixCsvGenomeInformationAffymetrixFileAffymetrixFileSetAffymetrixFileSetReporterAffymetrixNetAffxCsvFileAffymetrixPgfFileAffymetrixPlatformAffymetrixProbeTabFileAffymetrixTabularFileAffymetrixTsvFileAlleleSummationAllelicCrosstalkCalibrationallocate.AromaCellMatchScoreFileallocate.CrlmmParametersFileallocateFromCdfallocateFromCdf.AffymetrixCelFileallocateFromCdf.AromaCellCpgFileallocateFromCdf.AromaCellMatchScoreFileallocateFromCdf.AromaCellPositionFileallocateFromCdf.AromaCellSequenceFileallocateFromCdf.AromaUfcFileallocateFromCdf.AromaUflFileallocateFromCdf.AromaUnitGcContentFileallocateFromCdf.AromaUnitTabularBinaryFileannotateMvsAannotateMvsA.AffymetrixCelFileappend.AffymetrixCelSetappend.CnagCfhSetapplyAnyOrderapplyAnyOrder.CopyNumberChromosomalModelapplyCCF0applyCCF0.CopyNumberChromosomalModelapplyCFC0applyCFC0.CopyNumberChromosomalModelapplyToUnitIntensitiesapplyToUnitIntensities.AffymetrixCelSetaroma.affymetrixAromaAffymetrixAromaCellMatchScoreFileAromaChipTypeAnnotationFileAromaPipelineAromaUfcFileArrayExploreras.AffymetrixCelSetas.AffymetrixCelSet.AffymetrixCelSetas.AffymetrixCelSet.defaultas.AffymetrixCelSet.listas.AffymetrixCnChpSetas.AffymetrixCnChpSet.AffymetrixCnChpSetas.AffymetrixCnChpSet.defaultas.AffymetrixCnChpSet.listas.AffymetrixFileSetas.AffymetrixFileSet.AffymetrixFileSetas.AffymetrixFileSet.defaultas.AffymetrixFileSet.listas.character.AffymetrixCdfFileas.character.AffymetrixCelFileas.character.AffymetrixCelSetas.character.AffymetrixCelSetReporteras.character.AffymetrixCnChpFileas.character.AffymetrixCnChpSetas.character.AffymetrixPgfFileas.character.AffymetrixProbeTabFileas.character.AromaChipTypeAnnotationFileas.character.ArrayExploreras.character.ChipEffectFileas.character.ChipEffectSetas.character.CnagCfhFileas.character.CnagCfhSetas.character.DChipCdfBinFileas.character.DChipDcpFileas.character.DChipDcpSetas.character.DChipQuantileNormalizationas.character.FirmaModelas.character.GenericReporteras.character.GenomeInformationas.character.Modelas.character.ProbeAffinityFileas.character.QualityAssessmentModelas.character.ResidualFileas.character.ResidualSetas.character.SmoothMultiarrayModelas.character.SnpInformationas.character.SpatialReporteras.character.TransformReportas.character.WeightsFileas.character.WeightsSetas.ChipEffectSetTupleas.ChipEffectSetTuple.ChipEffectSetTupleas.ChipEffectSetTuple.defaultas.CnagCfhSetas.CnagCfhSet.CnagCfhSetas.CnagCfhSet.defaultas.CnagCfhSet.listas.CnChipEffectSetTupleas.CnChipEffectSetTuple.CnChipEffectSetTupleas.CnChipEffectSetTuple.defaultas.CopyNumberDataSetTuple.CnChipEffectSetas.DChipDcpSetas.DChipDcpSet.DChipDcpSetas.DChipDcpSet.defaultas.DChipDcpSet.listASCRMAv2assertAnnotationDataassertAnnotationData.ASCRMAv2averageQuantileaverageQuantile.AffymetrixCelSetAvgCnPlmAvgPlmAvgSnpPlmBackgroundCorrectionBaseCountNormalizationBasePositionNormalizationboxplotStatsboxplotStats.ChipEffectSetbpmapCluster2CdfbpmapCluster2Cdf.defaultbyChipType.AffymetrixCsvGenomeInformationbyChipType.AffymetrixProbeTabFilebyChipType.AffymetrixTabularFilebyChipType.AffymetrixTsvFilebyChipType.AromaCellMatchScoreFilebyChipType.AromaChipTypeAnnotationFilebyChipType.DChipCdfBinFilebyChipType.DChipGenomeInformationbyChipType.DChipSnpInformationbyChipType.GenomeInformationbyChipType.SnpInformationbyChipType.UflSnpInformationbyChipType.UgpGenomeInformationbyName.AffymetrixCelSetbyName.AffymetrixCnChpSetbyName.AromaChipTypeAnnotationFilebyName.CnagCfhSetbyName.CrlmmParametersSetbyName.DChipDcpSetbyPath.AffymetrixCelSetbyPath.AffymetrixCelSetTuplebyPath.AffymetrixCnChpSetbyPath.AffymetrixFileSetbyPath.ChipEffectSetbyPath.CnagCfhSetbyPath.CnChipEffectSetbyPath.CrlmmParametersSetbyPath.DChipDcpSetbyPath.ExonChipEffectSetbyPath.FirmaSetbyPath.ResidualSetbyPath.SnpChipEffectSetbyPath.WeightsSetcalcRawCnStatscalcRawCnStats.CopyNumberChromosomalModelcalcRawCnStats.defaultcalculateAffinitiescalculateAffinities.GcRmaBackgroundCorrectioncalculateAveragescalculateAverages.FragmentEquivalentClassNormalizationcalculateBaselinecalculateBaseline.ChipEffectSetcalculateConfidenceScorescalculateConfidenceScores.CrlmmModelcalculateFieldBoxplotStatscalculateFieldBoxplotStats.ChipEffectSetcalculateMarginscalculateMargins.SpatialReportercalculateNuseBoxplotStatscalculateNuseBoxplotStats.ChipEffectSetcalculateParametersGsbcalculateParametersGsb.AffymetrixCelSetcalculateResidualSetcalculateResidualSet.FirmaModelcalculateResidualSet.ProbeLevelModelcalculateRleBoxplotStatscalculateRleBoxplotStats.ChipEffectSetcalculateTargetDistributioncalculateTargetDistribution.QuantileNormalizationcalculateWeightscalculateWeights.ExonRmaPlmcalculateWeights.FirmaModelcalculateWeights.ProbeLevelModelcalibrateOnecalibrateOne.ReseqCrosstalkCalibrationcdfMergeGroupsChipEffectFileChipEffectGroupMergeChipEffectSetChipEffectSetTupleChipEffectTransformclearCache.AffymetrixCelSetclearDataclearData.AffymetrixCelFileclone.AffymetrixCelFileclone.AffymetrixCelSetclone.AffymetrixCnChpFileclone.CnagCfhFileclone.CnagCfhSetCnagCfhFileCnagCfhSetCnChipEffectFileCnChipEffectSetCnChipEffectSetTupleCnPlmCnProbeAffinityFilecomparecompare.AffymetrixCdfFilecomputeAffinitiescomputeAffinities.AffymetrixCdfFilecomputeAffinitiesByACScomputeAffinitiesByACS.AffymetrixCdfFileconvertconvert.AffymetrixCdfFileconvertToUniqueconvertToUnique.AffymetrixCelSetconvertUnitsconvertUnits.AffymetrixCdfFilecreateExonByTranscriptCdfcreateExonByTranscriptCdf.AffymetrixCdfFilecreateFromcreateFrom.AffymetrixCelFilecreateMonocellCdfcreateMonocellCdf.AffymetrixCdfFilecreateOutputTuplecreateOutputTuple.SmoothMultiarrayModelcreateParamCdfcreateParamCdf.ChipEffectFilecreateParamCdf.FirmaFilecreateUniqueCdfcreateUniqueCdf.AffymetrixCdfFileCrlmmModelCrlmmParametersFileCrlmmParametersSetDChipCdfBinFileDChipDcpFileDChipDcpSetDChipGenomeInformationDChipQuantileNormalizationDChipSnpInformationdecodedecode.ParameterCelFiledim.DChipDcpFiledoASCRMAv1doASCRMAv1.defaultdoASCRMAv2doASCRMAv2.defaultdoCRMAv1doCRMAv1.AffymetrixCelSetdoCRMAv1.defaultdoCRMAv2doCRMAv2.AffymetrixCelSetdoCRMAv2.defaultdoFIRMAdoFIRMA.AffymetrixCelSetdoFIRMA.defaultdoGCRMAdoGCRMA.AffymetrixCelSetdoGCRMA.defaultdoRMAdoRMA.AffymetrixCelSetdoRMA.defaultdropCellsFromCdfListencodeencode.ParameterCelFileenv2CdfEnv2CdfexcludeChrXFromFitexcludeChrXFromFit.DChipQuantileNormalizationExonChipEffectFileExonChipEffectSetExonProbeAffinityFileExonRmaPlmexportAromaSignalBinaryFileListexportAromaSignalBinaryFileList.CnChipEffectFileexportTotalAndFracBexportTotalAndFracB.CnChipEffectFileexportTotalAndFracB.CnChipEffectSetexportTotalAndFracB.DChipDcpSetexportTotalAndFracB.SnpChipEffectFileexportTotalAndFracB.SnpChipEffectSetexportTotalCnRatioSet.AffymetrixCnChpSetextractAffyBatchextractAffyBatch.AffymetrixCelSetextractAffyBatch.ChipEffectSetextractAlleleSetextractAlleleSet.SnpChipEffectSetextractChromosomalDataFrameextractChromosomalDataFrame.ChipEffectFileextractChromosomalDataFrame.ChipEffectSetextractCNTextractCNT.SnpChipEffectFileextractCNT.SnpChipEffectSetextractDataFrameextractDataFrame.ParameterCelFileextractDataFrame.ParameterCelSetextractExpressionSetextractExpressionSet.ChipEffectSetextractFeatureSetextractFeatureSet.AffymetrixCelSetextractLogRatiosextractLogRatios.AffymetrixCnChpFileextractLogRatios.AffymetrixCnChpSetextractMatrix.AffymetrixCelFileextractMatrix.AffymetrixCelSetextractMatrix.ChipEffectFileextractMatrix.ChipEffectSetextractMatrix.FirmaFileextractMatrix.FirmaSetextractMatrix.ParameterCelFileextractMatrix.ParameterCelSetextractSnpCnvQSetextractSnpCnvQSet.SnpChipEffectSetextractSnpFeatureSetextractSnpFeatureSet.AffymetrixCelSetextractSnpQSetextractSnpQSet.SnpChipEffectSetextractThetaextractTheta.ChipEffectFileextractTheta.ChipEffectSetextractTheta.CnChipEffectFileextractTheta.CnChipEffectSetextractTheta.DChipDcpFileextractTheta.DChipDcpSetextractTheta.SnpChipEffectFileextractTheta.SnpChipEffectSetextractTheta.SnpCnvQSetextractTheta.SnpQSetextractTotalAndFracBextractTotalAndFracB.SnpChipEffectFileextractTotalAndFreqBextractTotalAndFreqB.CnChipEffectFileextractTotalAndFreqB.CnChipEffectSetextractTotalAndFreqB.defaultextractTotalAndFreqB.SnpChipEffectSetfindByCdf2findByCdf2.defaultfindByChipType.AffymetrixCdfFilefindByChipType.AffymetrixCsvFilefindByChipType.AffymetrixCsvGenomeInformationfindByChipType.AffymetrixNetAffxCsvFilefindByChipType.AffymetrixPgfFilefindByChipType.AffymetrixProbeTabFilefindByChipType.AffymetrixTabularFilefindByChipType.AffymetrixTsvFilefindByChipType.AromaChipTypeAnnotationFilefindByChipType.DChipCdfBinFilefindByChipType.DChipGenomeInformationfindByChipType.DChipSnpInformationfindByChipType.UflSnpInformationfindByChipType.UgpGenomeInformationfindByName.AffymetrixCelSetfindByName.AffymetrixCnChpSetfindByName.ChipEffectSetfindByName.CnagCfhSetfindByName.DChipDcpSetfindTargetDistributionFilefindTargetDistributionFile.QuantileNormalizationfindUnitsTodo.AlleleSummationfindUnitsTodo.ChipEffectFilefindUnitsTodo.ChipEffectSetfindUnitsTodo.CrlmmModelfindUnitsTodo.CrlmmParametersFilefindUnitsTodo.CrlmmParametersSetfindUnitsTodo.ExonChipEffectSetfindUnitsTodo.FirmaFilefindUnitsTodo.FirmaModelfindUnitsTodo.FirmaSetfindUnitsTodo.ProbeLevelModelfindUnitsTodo.QualityAssessmentFilefindUnitsTodo.ResidualFilefindUnitsTodo.ResidualSetfindUnitsTodo.UnitModelfindUnitsTodo.WeightsFilefindUnitsTodo.WeightsSetFirmaFileFirmaModelFirmaSetfit.CrlmmModelfit.FirmaModelfit.Modelfit.ProbeLevelModelfit.SingleArrayUnitModelfit.SmoothMultiarrayModelfitCnProbesfitCnProbes.UnitModelfitOnefitOne.AbstractProbeSequenceNormalizationfitOne.BaseCountNormalizationfitOne.LinearModelProbeSequenceNormalizationfitOne.MatNormalizationfitOne.ReseqCrosstalkCalibrationfitOne.ScaleNormalization3fitOne.UnitTypeScaleNormalizationfitOneArrayfitOneArray.SingleArrayUnitModelfitOneChromosomefitOneChromosome.SmoothMultiarrayModelfitPlasqUnitfitPlasqUnit.matrixfitQuantileNormFcnfitQuantileNormFcn.AffymetrixCelFilefixSearchPath.AromaAffymetrixFragmentEquivalentClassNormalizationFragmentLengthNormalizationfromCdffromCdf.AffymetrixProbeTabFilefromCdf.GenomeInformationfromCdf.SnpInformationfromDataFilefromDataFile.ChipEffectFilefromDataFile.FirmaFilefromDataFile.ResidualFilefromDataFile.WeightsFilefromDataSetfromDataSet.ChipEffectSetfromDataSet.FirmaSetfromDataSet.GenomeInformationfromDataSet.ResidualSetfromDataSet.SnpInformationfromDataSet.WeightsSetfromFile.AffymetrixCdfFilefromFile.AffymetrixCelFilefromFile.AffymetrixCnChpFilefromFile.AffymetrixPgfFilefromFile.AromaChipTypeAnnotationFilefromFile.CnagCfhFilefromFile.DChipCdfBinFilefromFile.DChipDcpFileGcContentNormalizationGcContentNormalization2GcRmaBackgroundCorrectionGenericReporterGenomeInformationgetACSFilegetACSFile.AffymetrixCdfFilegetAlias.ArrayExplorergetAlias.GenericReportergetAlias.ModelgetAlias.TransformReportgetAlleleCellPairsgetAlleleCellPairs.AffymetrixCdfFilegetAlleleProbePairsgetAlleleProbePairs.AffymetrixCdfFilegetAlleleProbePairs2getAlleleProbePairs2.AffymetrixCdfFilegetAlleleProbePairs3getAlleleProbePairs3.AffymetrixCdfFilegetAmgetAm.AffymetrixCelFilegetAM.ChipEffectFilegetAM.ChipEffectSetgetAromaCellMatchScoreFilegetAromaCellMatchScoreFile.MatNormalizationgetAromaCellPositionFilegetAromaCellPositionFile.MatSmoothinggetAromaCellSequenceFilegetAromaCellSequenceFile.AbstractProbeSequenceNormalizationgetAromaCellSequenceFile.AffymetrixCdfFilegetAromaUfcFilegetAromaUfcFile.FragmentEquivalentClassNormalizationgetAromaUflFile.UflSnpInformationgetAromaUgpFile.UgpGenomeInformationgetAromaUnitFracBCnBinarySetgetAromaUnitFracBCnBinarySet.defaultgetAromaUnitTotalCnBinarySetgetAromaUnitTotalCnBinarySet.defaultgetArrayNamesgetArrayNames.AffymetrixAptSummaryFilegetArraysOfInput.ArrayExplorergetAsFullCelFilegetAsFullCelFile.ChipEffectFilegetAsFullCelSetgetAsFullCelSet.ChipEffectSetgetAsteriskTags.AdditiveCovariatesNormalizationgetAsteriskTags.AffineCnPlmgetAsteriskTags.AffinePlmgetAsteriskTags.AffineSnpPlmgetAsteriskTags.AlleleSummationgetAsteriskTags.AllelicCrosstalkCalibrationgetAsteriskTags.ArrayExplorergetAsteriskTags.AvgCnPlmgetAsteriskTags.AvgPlmgetAsteriskTags.AvgSnpPlmgetAsteriskTags.BaseCountNormalizationgetAsteriskTags.BasePositionNormalizationgetAsteriskTags.CrlmmModelgetAsteriskTags.ExonRmaPlmgetAsteriskTags.FirmaModelgetAsteriskTags.FragmentEquivalentClassNormalizationgetAsteriskTags.FragmentLengthNormalizationgetAsteriskTags.GenericReportergetAsteriskTags.HetLogAddCnPlmgetAsteriskTags.HetLogAddPlmgetAsteriskTags.HetLogAddSnpPlmgetAsteriskTags.LimmaBackgroundCorrectiongetAsteriskTags.MatNormalizationgetAsteriskTags.MbeiCnPlmgetAsteriskTags.MbeiPlmgetAsteriskTags.MbeiSnpPlmgetAsteriskTags.ModelgetAsteriskTags.NormExpBackgroundCorrectiongetAsteriskTags.ProbeLevelModelgetAsteriskTags.ProbeLevelTransform3getAsteriskTags.QualityAssessmentModelgetAsteriskTags.ReseqCrosstalkCalibrationgetAsteriskTags.RmaCnPlmgetAsteriskTags.RmaPlmgetAsteriskTags.RmaSnpPlmgetAsteriskTags.ScaleNormalizationgetAsteriskTags.SmoothMultiarrayModelgetAsteriskTags.SmoothRmaModelgetAsteriskTags.SmoothSaModelgetAsteriskTags.SnpChipEffectGroupMergegetAsteriskTags.UnitModelgetAveragegetAverage.AffymetrixCelSetgetAverage.CnagCfhSetgetAverageAsinhgetAverageAsinh.AffymetrixCelSetgetAverageAsinh.CnagCfhSetgetAverageFile.AffymetrixCelSetgetAverageFile.ChipEffectSetgetAverageFile.CnagCfhSetgetAverageFile.CnChipEffectSetgetAverageFile.ExonChipEffectSetgetAverageFile.ResidualSetgetAverageFile.SnpChipEffectSetgetAverageFile.WeightsSetgetAverageLoggetAverageLog.AffymetrixCelSetgetAverageLog.CnagCfhSetgetBandwidthgetBandwidth.SmoothMultiarrayModelgetBaselinegetBaseline.ChipEffectSetgetBaseline.CnChipEffectSetgetBaseline.SnpChipEffectSetgetBlockSizesgetBlockSizes.SpatialRowColumnNormalizationgetCalculateResidualsFunctiongetCalculateResidualsFunction.AvgPlmgetCalculateResidualsFunction.ProbeLevelModelgetCalculateResidualsFunction.RmaPlmgetCalls.DChipDcpFilegetCallSetgetCallSet.CrlmmModelgetCdfgetCdf.AdditiveCovariatesNormalizationgetCdf.AffymetrixCelFilegetCdf.AffymetrixCelSetgetCdf.AffymetrixCnChpFilegetCdf.AffymetrixCnChpSetgetCdf.AffymetrixProbeTabFilegetCdf.AffymetrixTsvFilegetCdf.AromaUnitTabularBinaryFilegetCdf.ChipEffectGroupMergegetCdf.CnagCfhFilegetCdf.CnagCfhSetgetCdf.FirmaModelgetCdf.FragmentEquivalentClassNormalizationgetCdf.FragmentLengthNormalizationgetCdf.GcContentNormalizationgetCdf.ModelgetCdf.QualityAssessmentModelgetCdf.TransformReportgetCdfBingetCdfBin.DChipDcpSetgetCellDimgetCellDim.DChipCdfBinFilegetCellIndicesgetCellIndices.AffymetrixCdfFilegetCellIndices.ChipEffectFilegetCellIndices.ChipEffectSetgetCellIndices.CnChipEffectFilegetCellIndices.CnPlmgetCellIndices.CnProbeAffinityFilegetCellIndices.ExonChipEffectFilegetCellIndices.ExonProbeAffinityFilegetCellIndices.ExonRmaPlmgetCellIndices.FirmaFilegetCellIndices.FirmaSetgetCellIndices.ProbeAffinityFilegetCellIndices.ResidualFilegetCellIndices.ResidualSetgetCellIndices.SnpChipEffectFilegetCellIndices.SnpPlmgetCellIndices.SnpProbeAffinityFilegetCellIndices.UnitModelgetCellIndices.WeightsFilegetCellIndices.WeightsSetgetCellMapForMainCdfgetCellMapForMainCdf.ChipEffectFilegetCellQuartetsgetCellQuartets.AffymetrixCdfFilegetCellsTogetCellsTo.ProbeLevelTransform3getCellsToFitgetCellsToFit.ProbeLevelTransform3getCellsToInternalgetCellsToInternal.ProbeLevelTransform3getCellsToUpdategetCellsToUpdate.ProbeLevelTransform3getChipEffectFileClassgetChipEffectFileClass.ChipEffectSetgetChipEffectFileClass.CnChipEffectSetgetChipEffectFileClass.ExonChipEffectSetgetChipEffectFileClass.SnpChipEffectSetgetChipEffectSetgetChipEffectSet.AlleleSummationgetChipEffectSet.CnPlmgetChipEffectSet.ExonRmaPlmgetChipEffectSet.ProbeLevelModelgetChipEffectSet.QualityAssessmentModelgetChipEffectSet.SnpPlmgetChipEffectSetClassgetChipEffectSetClass.AlleleSummationgetChipEffectSetClass.CnPlmgetChipEffectSetClass.ExonRmaPlmgetChipEffectSetClass.ProbeLevelModelgetChipEffectSetClass.SnpPlmgetChipType.AffymetrixAptSummaryFilegetChipType.AffymetrixCdfFilegetChipType.AffymetrixCelFilegetChipType.AffymetrixCelSetgetChipType.AffymetrixCelSetReportergetChipType.AffymetrixCnChpFilegetChipType.AffymetrixPgfFilegetChipType.AffymetrixProbeTabFilegetChipType.AffymetrixTsvFilegetChipType.AromaChipTypeAnnotationFilegetChipType.CnagCfhFilegetChipType.CrlmmModelgetChipType.DChipCdfBinFilegetChipType.DChipDcpSetgetChipType.GenomeInformationgetChipType.SnpInformationgetChipType.UflSnpInformationgetChipType.UgpGenomeInformationgetChromosomes.GenomeInformationgetChromosomes.UgpGenomeInformationgetChromosomeStatsgetChromosomeStats.GenomeInformationgetCnNamesgetCnNames.AffymetrixCdfFilegetColorMapsgetColorMaps.ArrayExplorergetColorMaps.SpatialReportergetColumnNames.AffymetrixProbeTabFilegetCombineAllelesgetCombineAlleles.CnChipEffectSetgetCombineAlleles.CnPlmgetConfidenceScoreSetgetConfidenceScoreSet.CrlmmModelgetCovariatesgetCovariates.AdditiveCovariatesNormalizationgetCovariates.GcContentNormalization2getCrlmmParametersSetgetCrlmmParametersSet.CrlmmModelgetCrlmmPriorsgetCrlmmPriors.CrlmmModelgetCrlmmSNPsgetCrlmmSNPs.CrlmmModelgetCrlmmSNPsOnChrXgetCrlmmSNPsOnChrX.CrlmmModelgetCrlmmSplineParametersgetCrlmmSplineParameters.CrlmmModelgetDatagetData.AffymetrixCelFilegetData.AffymetrixCelSetgetData.AffymetrixCnChpFilegetData.AffymetrixProbeTabFilegetData.AffymetrixTsvFilegetData.CnagCfhSetgetData.GenomeInformationgetData.SnpInformationgetData.UflSnpInformationgetData.UgpGenomeInformationgetDataColumnsgetDataColumns.GenomeInformationgetDataColumns.UflSnpInformationgetDataColumns.UgpGenomeInformationgetDataFlatgetDataFlat.ChipEffectFilegetDataFlat.FirmaFilegetDataFlat.ResidualFilegetDataFlat.WeightsFilegetDataPairsgetDataPairs.AllelicCrosstalkCalibrationgetDataSetgetDataSet.AffymetrixCelSetReportergetDataSet.ArrayExplorergetDataSet.FirmaModelgetDataSet.ModelgetDataSet.QualityAssessmentModelgetDefaultColumnNames.AromaCellMatchScoreFilegetDefaultColumnNames.AromaUfcFilegetDefaultExtension.AffymetrixCdfFilegetDefaultExtension.AffymetrixCsvFilegetDefaultExtension.AffymetrixCsvGenomeInformationgetDefaultExtension.AffymetrixNetAffxCsvFilegetDefaultExtension.AffymetrixPgfFilegetDefaultExtension.AffymetrixTsvFilegetDefaultExtension.AromaCellMatchScoreFilegetDefaultExtension.AromaChipTypeAnnotationFilegetDefaultFullName.AffymetrixFileSetgetDefaultFullName.CnagCfhSetgetDefaultSettingsgetDefaultSettings.AromaAffymetrixgetDefaultSettings.PackagegetDesignMatrixgetDesignMatrix.BaseCountNormalizationgetDesignMatrix.BasePositionNormalizationgetDesignMatrix.LinearModelProbeSequenceNormalizationgetDesignMatrix.MatNormalizationgetDimensiongetDimension.AffymetrixCdfFilegetDimension.AffymetrixPgfFilegetExclCellsgetExclCells.DChipQuantileNormalizationgetExclCells.QuantileNormalizationgetExcludesgetExcludes.DChipDcpFilegetExclusiveUnitSubsetsgetExclusiveUnitSubsets.FragmentEquivalentClassNormalizationgetExpandedCellMapgetExpandedCellMap.ChipEffectFilegetExpandedCellMap.CnChipEffectFilegetExpandedCellMap.SnpChipEffectFilegetExpectedOutputFullnames.MatSmoothinggetExtensionPattern.AffymetrixCdfFilegetExtensionPattern.AffymetrixCelFilegetExtensionPattern.AffymetrixCnChpFilegetExtensionPattern.AffymetrixCsvFilegetExtensionPattern.AffymetrixPgfFilegetExtensionPattern.AffymetrixTsvFilegetExtensionPattern.AromaCellMatchScoreFilegetExtensionPattern.AromaUfcFilegetExtensionPattern.CnagCfhFilegetExtensionPattern.DChipDcpFilegetFieldgetField.AffymetrixTsvFilegetFields.SnpInformationgetFields.UflSnpInformationgetFileClass.FirmaSetgetFileFormatgetFileFormat.AffymetrixCdfFilegetFileFormat.AffymetrixCelFilegetFileFormat.AffymetrixCnChpFilegetFileFormat.DChipCdfBinFilegetFileFormat.DChipDcpFilegetFilenameExtension.AromaCellMatchScoreFilegetFilenameExtension.AromaUfcFilegetFileSetgetFileSet.AffymetrixFileSetReportergetFileSetClassgetFileSetClass.FirmaModelgetFilteredFragmentLengthsgetFilteredFragmentLengths.FragmentLengthNormalizationgetFirmaScoresgetFirmaScores.FirmaModelgetFirmaSetgetFirmaSet.FirmaModelgetFirstCellIndicesgetFirstCellIndices.AffymetrixCdfFilegetFirstCellPerUnitIndicesgetFirstCellPerUnitIndices.ExonChipEffectSetgetFitgetFit.BasePositionNormalizationgetFitSingleCellUnitFunctiongetFitSingleCellUnitFunction.UnitModelgetFitUnitFunctiongetFitUnitFunction.CnPlmgetFitUnitFunction.FirmaModelgetFitUnitFunction.MultiArrayUnitModelgetFitUnitFunction.SingleArrayUnitModelgetFitUnitFunction.UnitModelgetFitUnitGroupFunctiongetFitUnitGroupFunction.AffinePlmgetFitUnitGroupFunction.AvgPlmgetFitUnitGroupFunction.ExonRmaPlmgetFitUnitGroupFunction.FirmaModelgetFitUnitGroupFunction.HetLogAddPlmgetFitUnitGroupFunction.MbeiPlmgetFitUnitGroupFunction.MultiArrayUnitModelgetFitUnitGroupFunction.RmaPlmgetFitUnitGroupFunction.SingleArrayUnitModelgetFitUnitGroupFunction.SmoothMultiarrayModelgetFitUnitGroupFunction.SmoothRmaModelgetFitUnitGroupFunction.SmoothSaModelgetFragmentLengthsgetFragmentLengths.AffymetrixTsvFilegetFragmentLengths.SnpInformationgetFragmentLengths.UflSnpInformationgetFragmentStartsgetFragmentStarts.SnpInformationgetFragmentStarts.UflSnpInformationgetFragmentStopsgetFragmentStops.SnpInformationgetFragmentStops.UflSnpInformationgetFullName.GenericReportergetFullName.ModelgetFullName.QualityAssessmentModelgetFullName.TransformReportgetFullNames.ChipEffectSetTuplegetGcgetGc.AffymetrixTsvFilegetGcContentgetGcContent.GcContentNormalizationgetGenomeBuildgetGenomeBuild.AffymetrixNetAffxCsvFilegetGenomeInformationgetGenomeInformation.AffymetrixCdfFilegetGroupDirectionsgetGroupDirections.AffymetrixCdfFilegetHeader.AffymetrixCdfFilegetHeader.AffymetrixCelFilegetHeader.AffymetrixCnChpFilegetHeader.AffymetrixPgfFilegetHeader.AromaChipTypeAnnotationFilegetHeader.CnagCfhFilegetHeader.DChipCdfBinFilegetHeader.DChipDcpFilegetHeaderAttributesgetHeaderAttributes.AffymetrixNetAffxCsvFilegetHeaderLengthgetHeaderLength.CnagCfhFilegetHeaderV3getHeaderV3.AffymetrixCelFilegetIdentifiergetIdentifier.AffymetrixCelFilegetIdentifier.AffymetrixCelSetgetIdentifier.AffymetrixFileSetgetIdentifier.CnagCfhFilegetIdentifier.CnagCfhSetgetImage.AffymetrixCdfFilegetImage.AffymetrixCelFilegetImage.AromaUnitTabularBinaryFilegetImage.ResidualFilegetImage.WeightsFilegetIndexToRowMapgetIndexToRowMap.AffymetrixProbeTabFilegetInputDataSet.TransformReportgetInputNamegetInputName.AffymetrixFileSetReportergetInputName.GenericReportergetInputTagsgetInputTags.AffymetrixFileSetReportergetInputTags.GenericReportergetIntensitiesgetIntensities.AffymetrixCelSetgetLabel.ModelgetListOfCdfsgetListOfCdfs.AffymetrixCelSetTuplegetListOfGenomeInformationsgetListOfGenomeInformations.ChromosomalModelgetListOfPriorsgetListOfPriors.MultiArrayUnitModelgetListOfReportersgetListOfReporters.ArrayExplorergetListOfUnitNamesFiles.AffymetrixCelSetTuplegetListOfUnitNamesFiles.ArrayExplorergetListOfUnitTypesFiles.AffymetrixCelSetTuplegetListOfUnitTypesFiles.ArrayExplorergetMainCdfgetMainCdf.AffymetrixCdfFilegetMainPath.GenericReportergetMergeFunctiongetMergeFunction.ChipEffectGroupMergegetMergeFunction.SnpChipEffectGroupMergegetMergeGroupsgetMergeGroups.ExonChipEffectSetgetMergeStrandsgetMergeStrands.SnpChipEffectSetgetMergeStrands.SnpPlmgetMonocellCdfgetMonocellCdf.AffymetrixCdfFilegetName.AffymetrixPlatformgetName.FirmaModelgetName.GenericReportergetName.ModelgetName.QualityAssessmentModelgetName.TransformReportgetNameOfInput.ArrayExplorergetNetAffxBuildgetNetAffxBuild.AffymetrixNetAffxCsvFilegetNetAffxDategetNetAffxDate.AffymetrixNetAffxCsvFilegetNormalEquationsgetNormalEquations.LinearModelProbeSequenceNormalizationgetNormalizedIntensitiesgetNormalizedIntensities.DChipDcpFilegetNormalizeSignalsOnegetNormalizeSignalsOne.ScaleNormalization3getNormalizeSignalsOne.UnitTypeScaleNormalizationgetNumberOfFilesAveraged.CnChipEffectFilegetOrderedFragmentPairMapgetOrderedFragmentPairMap.AromaUfcFilegetOrderedFragmentPairsgetOrderedFragmentPairs.AromaUfcFilegetOutputDataSet.TransformgetOutputDataSet.TransformReportgetOutputDataSet00getOutputDataSet00.AdditiveCovariatesNormalizationgetOutputDataSet00.FragmentEquivalentClassNormalizationgetOutputDataSet00.FragmentLengthNormalizationgetOutputDataSet00.GcContentNormalizationgetOutputFiles.TransformgetOutputIdentifiergetOutputIdentifier.QuantileNormalizationgetOutputTuplegetOutputTuple.SmoothMultiarrayModelgetParametergetParameter.AffymetrixAptSummaryFilegetParameters.AbstractProbeSequenceNormalizationgetParameters.AdditiveCovariatesNormalizationgetParameters.AllelicCrosstalkCalibrationgetParameters.AvgPlmgetParameters.BackgroundCorrectiongetParameters.BaseCountNormalizationgetParameters.BasePositionNormalizationgetParameters.ChipEffectFilegetParameters.ChipEffectGroupMergegetParameters.CnChipEffectFilegetParameters.CnPlmgetParameters.CrlmmModelgetParameters.DChipQuantileNormalizationgetParameters.ExonChipEffectFilegetParameters.ExonRmaPlmgetParameters.FragmentEquivalentClassNormalizationgetParameters.FragmentLengthNormalizationgetParameters.GcContentNormalizationgetParameters.GcRmaBackgroundCorrectiongetParameters.LimmaBackgroundCorrectiongetParameters.MatNormalizationgetParameters.MatSmoothinggetParameters.NormExpBackgroundCorrectiongetParameters.OpticalBackgroundCorrectiongetParameters.ProbeAffinityFilegetParameters.ProbeLevelTransform3getParameters.QuantileNormalizationgetParameters.ReseqCrosstalkCalibrationgetParameters.ResidualFilegetParameters.ResidualSetgetParameters.RmaBackgroundCorrectiongetParameters.RmaPlmgetParameters.ScaleNormalizationgetParameters.ScaleNormalization3getParameters.SnpChipEffectFilegetParameters.SnpChipEffectGroupMergegetParameters.SnpPlmgetParameters.SpatialRowColumnNormalizationgetParameters.UnitModelgetParameters.UnitTypeScaleNormalizationgetParameters.WeightsFilegetParameters.WeightsSetgetPath.AffymetrixCelSetReportergetPath.GenericReportergetPath.ModelgetPath.QualityAssessmentModelgetPath.TransformReportgetPcuThetagetPcuTheta.ChromosomalModelgetPlasqTypesgetPlatform.AffymetrixCdfFilegetPlatform.AffymetrixCelFilegetPlatform.AffymetrixCelSetgetPlatform.AffymetrixPgfFilegetPlatform.AromaChipTypeAnnotationFilegetPlatform.DChipCdfBinFilegetPlatformDesignDBgetPlatformDesignDB.CrlmmModelgetPlmgetPlm.FirmaModelgetPlm.QualityAssessmentModelgetPosition.AffymetrixTsvFilegetPositionChipTypeUnitgetPositionChipTypeUnit.ChromosomalModelgetPositionChipTypeUnit.CopyNumberSegmentationModelgetPositions.GenomeInformationgetProbeAffinityFilegetProbeAffinityFile.AffinePlmgetProbeAffinityFile.AvgPlmgetProbeAffinityFile.CnPlmgetProbeAffinityFile.ExonRmaPlmgetProbeAffinityFile.MbeiPlmgetProbeAffinityFile.ProbeLevelModelgetProbeAffinityFile.RmaPlmgetProbeAffinityFile.SnpPlmgetProbeSequenceDatagetProbeSequenceData.AffymetrixCdfFilegetProbesetIdsgetProbesetIds.AffymetrixAptSummaryFilegetQuantificationScalegetQuantificationScale.AffymetrixAptSummaryFilegetRawIntensitiesgetRawIntensities.DChipDcpFilegetReadArguments.AffymetrixAptSummaryFilegetRectanglegetRectangle.AffymetrixCelFilegetReference.SpatialReportergetRegions.profileCGHgetReportSetgetReportSet.GenericReportergetReportSet.SpatialReportergetResidualFileClassgetResidualFileClass.ResidualSetgetResidualsgetResiduals.QualityAssessmentModelgetResidualSetgetResidualSet.ProbeLevelModelgetResidualSetClassgetResidualSetClass.ProbeLevelModelgetRestructorgetRestructor.AffymetrixCdfFilegetRlmFitFunctionsgetRlmFitFunctions.RmaPlmgetRootPath.AlleleSummationgetRootPath.ChipEffectTransformgetRootPath.CrlmmModelgetRootPath.FirmaModelgetRootPath.GenericReportergetRootPath.ModelgetRootPath.ProbeLevelModelgetRootPath.ProbeLevelTransformgetRootPath.QualityAssessmentModelgetRootPath.SmoothMultiarrayModelgetRootPath.SmoothRmaModelgetRootPath.TransformReportgetSetsOfProbesgetSetsOfProbes.AllelicCrosstalkCalibrationgetSetsOfProbes.ReseqCrosstalkCalibrationgetSettingsgetSettings.PackagegetSetTuple.ArrayExplorergetSignalTransformgetSignalTransform.BasePositionNormalizationgetSignalTransform.LinearModelProbeSequenceNormalizationgetSnpInformationgetSnpInformation.AffymetrixCdfFilegetSnpNamesgetSnpNames.AffymetrixCdfFilegetSpargetSpar.SpatialRowColumnNormalizationgetStepsgetSteps.AromaPipelinegetSteps.ASCRMAv2getSubsetOfCellIndicesgetSubsetOfCellIndices.AffymetrixCdfFilegetSubsetOfUnitsgetSubsetOfUnits.AffymetrixCdfFilegetSubsetToAvggetSubsetToAvg.AllelicCrosstalkCalibrationgetSubsetToAvg.QuantileNormalizationgetSubsetToAvg.ReseqCrosstalkCalibrationgetSubsetToAvg.ScaleNormalizationgetSubsetToFitgetSubsetToFit.AdditiveCovariatesNormalizationgetSubsetToFit.FragmentEquivalentClassNormalizationgetSubsetToFit.FragmentLengthNormalizationgetSubsetToFit.GcContentNormalizationgetSubsetToUpdategetSubsetToUpdate.BackgroundCorrectiongetSubsetToUpdate.DChipQuantileNormalizationgetSubsetToUpdate.QuantileNormalizationgetSubsetToUpdate.ScaleNormalizationgetSubsetToUpdate0getSubsetToUpdate0.LimmaBackgroundCorrectiongetTags.FirmaModelgetTags.GenericReportergetTags.ModelgetTags.QualityAssessmentModelgetTags.TransformReportgetTagsOfInput.ArrayExplorergetTargetAveragesgetTargetAverages.FragmentEquivalentClassNormalizationgetTargetDistributiongetTargetDistribution.QuantileNormalizationgetTargetDistributionIdentifiergetTargetDistributionIdentifier.QuantileNormalizationgetTargetDistributionPathnamegetTargetDistributionPathname.QuantileNormalizationgetTargetFilegetTargetFile.AbstractProbeSequenceNormalizationgetTargetFunctiongetTargetFunction.GcContentNormalizationgetTargetFunctionsgetTargetFunctions.AdditiveCovariatesNormalizationgetTargetFunctions.FragmentLengthNormalizationgetThetasgetThetas.DChipDcpFilegetThetasABgetThetasAB.DChipDcpFilegetThetaStdsgetThetaStds.DChipDcpFilegetTimestampgetTimeStampgetTimeStamp.AffymetrixAptSummaryFilegetTimestamp.AffymetrixCelFilegetTimestamp.AffymetrixCnChpFilegetTimestamp.CnagCfhFilegetTimestampsgetTimestamps.AffymetrixCelSetgetTimestamps.CnagCfhSetgetUniqueCdfgetUniqueCdf.AffymetrixCdfFilegetUnitGroupCellArrayMapgetUnitGroupCellArrayMap.ChipEffectFilegetUnitGroupCellChromosomePositionMapgetUnitGroupCellChromosomePositionMap.AffymetrixCdfFilegetUnitGroupCellChromosomePositionMap.ChipEffectFilegetUnitGroupCellMapgetUnitGroupCellMap.AffymetrixCdfFilegetUnitGroupCellMap.AffymetrixCelSetgetUnitGroupCellMap.ChipEffectFilegetUnitGroupCellMap.FirmaFilegetUnitGroupCellMap.ResidualFilegetUnitGroupCellMap.WeightsFilegetUnitGroupCellMapWithMonocellgetUnitGroupCellMapWithMonocell.AffymetrixCdfFilegetUnitGroupCellMapWithUniquegetUnitGroupCellMapWithUnique.AffymetrixCdfFilegetUnitGroupCellMatrixMapgetUnitGroupCellMatrixMap.ChipEffectFilegetUnitGroupNamesFromUgcMapgetUnitGroupNamesFromUgcMap.AffymetrixCdfFilegetUnitIndicesgetUnitIndices.GenomeInformationgetUnitIntensitiesgetUnitIntensities.AffymetrixCelSetgetUnitNames.AffymetrixCdfFilegetUnitNames.AffymetrixNetAffxCsvFilegetUnitNames.AffymetrixPgfFilegetUnitNames.DChipCdfBinFilegetUnitNamesFile.AffymetrixCdfFilegetUnitNamesFile.AffymetrixCelFilegetUnitNamesFile.AffymetrixCelSetgetUnitNamesFile.AffymetrixCnChpFilegetUnitNamesFile.AffymetrixPgfFilegetUnitNamesFile.AffymetrixPlatformgetUnitNamesFile.TransformReportgetUnitReadMapgetUnitReadMap.AffymetrixCnChpFilegetUnitSizesgetUnitSizes.DChipCdfBinFilegetUnitsOnChromosome.GenomeInformationgetUnitsOnChromosome.UgpGenomeInformationgetUnitsOnChromosomes.GenomeInformationgetUnitsTogetUnitsTo.ProbeLevelTransform3getUnitsToFitgetUnitsToFit.CrlmmModelgetUnitsToFit.ProbeLevelTransform3getUnitsToUpdategetUnitsToUpdate.ProbeLevelTransform3getUnitTypes.AffymetrixCdfFilegetUnitTypesFile.AffymetrixCdfFilegetUnitTypesFile.AffymetrixCelFilegetUnitTypesFile.AffymetrixCelSetgetUnitTypesFile.AffymetrixCnChpFilegetUnitTypesFile.AffymetrixPlatformgetUnitTypesFile.TransformReportgetWeights.QualityAssessmentModelgetWeightsFileClassgetWeightsFileClass.WeightsSetgetWeightsSetgetWeightsSet.ProbeLevelModelgetWeightsSetClassgetWeightsSetClass.ProbeLevelModelgetXAM.ChipEffectFilegetXAM.ChipEffectSetgetYYgetYY.TransformReportgroupUnitsByDimensiongroupUnitsByDimension.AffymetrixCdfFilehasAlleleBFractions.CnChipEffectFilehasAlleleBFractions.CnChipEffectSethasAlleleBFractions.CnChipEffectSetTuplehasColumnHeader.AffymetrixProbeTabFilehasMbeiDatahasMbeiData.DChipDcpFilehasNormalizedDatahasNormalizedData.DChipDcpFilehasStrandiness.CnChipEffectFilehasStrandiness.CnChipEffectSethasStrandiness.CnChipEffectSetTuplehasUnitReadMaphasUnitReadMap.AffymetrixCnChpFilehasUnitTypeshasUnitTypes.AffymetrixCdfFileHetLogAddCnPlmHetLogAddPlmHetLogAddSnpPlmhighlighthighlight.AffymetrixCelFileidentifyCellsidentifyCells.AffymetrixCdfFileimage270image270.AffymetrixCelFileimportFrom.AromaUnitTabularBinaryFileimportFromAffymetrixNetAffxCsvFileimportFromAffymetrixNetAffxCsvFile.AromaUflFileimportFromAffymetrixNetAffxCsvFile.AromaUgpFileimportFromAffymetrixNetAffxCsvFile.AromaUnitGcContentFileimportFromAffymetrixNetAffxCsvFile.AromaUnitTabularBinaryFileimportFromAffymetrixProbeTabFileimportFromAffymetrixProbeTabFile.AromaCellSequenceFileimportFromAffymetrixTabularFileimportFromAffymetrixTabularFile.AromaUfcFileimportFromAffymetrixTabularFile.AromaUgpFileimportFromAffymetrixTabularFile.AromaUnitTabularBinaryFileimportFromAptimportFromApt.CnChipEffectSetimportFromBpMapimportFromBpMap.AromaCellMatchScoreFileimportFromBpMap.AromaCellSequenceFileimportFromDChipimportFromDChip.AffymetrixCelSetimportFromDChip.CnChipEffectSetimportFromDChipGenomeInformationimportFromDChipGenomeInformation.AromaUnitTabularBinaryFileimportFromGenericTabularFile.AromaUnitTabularBinaryFileimportFromGenomeInformationimportFromGenomeInformation.AromaUgpFileimportFromGenomeInformation.AromaUnitTabularBinaryFileindexOfMissingSequencesindexOfMissingSequences.AbstractProbeSequenceNormalizationinferMmFromPminferMmFromPm.AromaCellSequenceFileinferParametersinferParameters.CnChipEffectSetinferParameters.SnpChipEffectSetisCompatibleWithCdfisCompatibleWithCdf.GenomeInformationisCompatibleWithCdf.SnpInformationisCompatibleWithCdf.UflSnpInformationisCompatibleWithCdf.UgpGenomeInformationisDuplicatedisDuplicated.AffymetrixCelSetisDuplicated.CnagCfhSetisMissing.AromaCellMatchScoreFileisMonocellCdfisMonocellCdf.AffymetrixCdfFileisPmisPm.AffymetrixCdfFileisResequenceChipisResequenceChip.AffymetrixCdfFileisSnpChipisSnpChip.AffymetrixCdfFileisUniqueCdfisUniqueCdf.AffymetrixCdfFileisUnitGroupCellMapisUnitGroupCellMap.data.frameisUnitGroupCellMap.defaultisUnitGroupCellMap.matrixjustRMAjustRMA.AffymetrixCelSetjustRMA.defaultjustSNPRMAjustSNPRMA.AffymetrixCelSetjustSNPRMA.characterLimmaBackgroundCorrectionLinearModelProbeSequenceNormalizationmapToUnitNamesFilemapToUnitNamesFile.DChipCdfBinFileMatNormalizationMatSmoothingMbeiCnPlmMbeiPlmMbeiSnpPlmmergeGroupsmergeGroups.ChipEffectFilemergeStrandsmergeStrands.CnChipEffectFilemergeStrands.SnpChipEffectFilemigrateToolmigrateTool.CopyNumberSegmentationModelModelMultiArrayUnitModelnbrOfArrays.AffymetrixAptSummaryFilenbrOfArrays.AffymetrixCelSetnbrOfArrays.AffymetrixCelSetReporternbrOfArrays.AffymetrixCnChpSetnbrOfArrays.CnagCfhSetnbrOfArrays.DChipDcpSetnbrOfArrays.QualityAssessmentModelnbrOfArrays.TransformReportnbrOfCells.AffymetrixCdfFilenbrOfCells.AffymetrixCelFilenbrOfCells.AffymetrixPgfFilenbrOfCells.CnagCfhFilenbrOfCells.DChipCdfBinFilenbrOfCells.DChipDcpFilenbrOfCellsPerUnitnbrOfCellsPerUnit.AffymetrixCdfFilenbrOfCellsPerUnitGroupnbrOfCellsPerUnitGroup.AffymetrixCdfFilenbrOfChipTypes.ArrayExplorernbrOfColumns.AffymetrixCdfFilenbrOfColumns.AffymetrixPgfFilenbrOfEnzymes.AromaUfcFilenbrOfEnzymes.SnpInformationnbrOfEnzymes.UflSnpInformationnbrOfGroupsPerUnitnbrOfGroupsPerUnit.AffymetrixCdfFilenbrOfQcUnitsnbrOfQcUnits.AffymetrixCdfFilenbrOfRows.AffymetrixCdfFilenbrOfRows.AffymetrixPgfFilenbrOfSnpsnbrOfSnps.AffymetrixCdfFilenbrOfSnps.CnagCfhFilenbrOfStepsnbrOfSteps.AromaPipelinenbrOfUnits.AffymetrixCdfFilenbrOfUnits.AffymetrixPgfFilenbrOfUnits.DChipCdfBinFilenbrOfUnits.DChipDcpFilenbrOfUnits.GenomeInformationnbrOfUnits.SnpInformationnbrOfUnits.UflSnpInformationnbrOfUnits.UgpGenomeInformationnormalizeOneArrayVectornormalizeOneArrayVector.FragmentEquivalentClassNormalizationnormalizeQuantilenormalizeQuantile.AffymetrixCelFilenormalizeQuantile.AffymetrixCelSetNormExpBackgroundCorrectionOpticalBackgroundCorrectionParameterCelFileParameterCelSetpdInfo2CdfplasqGaussianplotAllelePairsplotAllelePairs.AllelicCrosstalkCalibrationplotBasepairplotBasepair.AllelicCrosstalkCalibrationplotBoxplotplotBoxplot.ChipEffectSetplotBoxplotStatsplotBoxplotStats.listplotCovariateEffectsplotCovariateEffects.GcContentNormalization2plotDensityplotDensity.AffymetrixCelFileplotDensity.AffymetrixCelSetplotDensity.GenomeInformationplotImageplotImage.AffymetrixCelFileplotMarginsplotMargins.SpatialReporterplotMvsAplotMvsA.AffymetrixCelFileplotMvsXplotMvsX.AffymetrixCelFileplotNuseplotNuse.QualityAssessmentModelplotRleplotRle.QualityAssessmentModelplotXYCurveplotXYCurve.TransformReportplotXYCurveLog2plotXYCurveLog2.TransformReportpredictOnepredictOne.AbstractProbeSequenceNormalizationpredictOne.BaseCountNormalizationpredictOne.LinearModelProbeSequenceNormalizationpredictOne.MatNormalizationProbeAffinityFileProbeLevelModelProbeLevelTransformProbeLevelTransform3process.AbstractProbeSequenceNormalizationprocess.AdditiveCovariatesNormalizationprocess.AlleleSummationprocess.AllelicCrosstalkCalibrationprocess.AromaPipelineprocess.ArrayExplorerprocess.BackgroundCorrectionprocess.ChipEffectGroupMergeprocess.DChipQuantileNormalizationprocess.FragmentEquivalentClassNormalizationprocess.FragmentLengthNormalizationprocess.GcContentNormalizationprocess.GcRmaBackgroundCorrectionprocess.GenericReporterprocess.LimmaBackgroundCorrectionprocess.MatNormalizationprocess.MatSmoothingprocess.OpticalBackgroundCorrectionprocess.QuantileNormalizationprocess.ReseqCrosstalkCalibrationprocess.RmaBackgroundCorrectionprocess.ScaleNormalizationprocess.ScaleNormalization3process.SpatialReporterprocess.SpatialRowColumnNormalizationprocess.UnitTypeScaleNormalizationQualityAssessmentFileQualityAssessmentModelQualityAssessmentSetQuantileNormalizationrandomSeedrange.AffymetrixCelFilerange.AffymetrixCelSetrange.CnagCfhFilerange.CnagCfhSetread10Kread10K.DChipSnpInformationread250Kread250K.DChipSnpInformationread250KHg17read250KHg17.DChipGenomeInformationread50Kread50K.DChipSnpInformationread50KHg17read50KHg17.DChipGenomeInformationreadArraysreadArrays.AffymetrixAptSummaryFilereadCdfGroupStrandsreadCfhHeaderreadCfhHeader.defaultreadCfhUnitsreadCfhUnits.defaultreadCfnHeaderreadCfnHeader.defaultreadCfnUnitsreadCfnUnits.defaultreadDataFrame.AffymetrixCdfFilereadDataFrame.AffymetrixCsvGenomeInformationreadDataFrame.AffymetrixTsvFilereadDataFrame.AromaUfcFilereadDataFrame.DChipCdfBinFilereadDataFrame.DChipGenomeInformationreadDataFrame.DChipSnpInformationreadDataFrame.GenomeInformationreadDataFrame.SnpInformationreadDataFrame.UflSnpInformationreadDataFrame.UgpGenomeInformationreadDataFrame2readDataFrame2.AffymetrixProbeTabFilereadDataUnitChromosomePositionreadDataUnitChromosomePosition.AffymetrixNetAffxCsvFilereadDataUnitFragmentLengthreadDataUnitFragmentLength.AffymetrixNetAffxCsvFilereadGeneAssignmentsreadGeneAssignments.AffymetrixNetAffxCsvFilereadGenomeWideSNPreadGenomeWideSNP.DChipGenomeInformationreadHeader.AffymetrixAptSummaryFilereadMatchScoresreadMatchScores.AromaCellMatchScoreFilereadMouse430readMouse430.DChipGenomeInformationreadMouse430KenHardwiredreadMouse430KenHardwired.DChipGenomeInformationreadParameterreadParameter.CrlmmParametersFilereadPlasqTypesreadPlasqTypes.AffymetrixCdfFilereadPriorsByUnitsreadPriorsByUnits.MultiArrayUnitModelreadProbesetIdsreadProbesetIds.AffymetrixAptSummaryFilereadRawDatareadRawData.AffymetrixCelFilereadRawData.AffymetrixCnChpFilereadRawData.AffymetrixPgfFilereadRawDataRectanglereadRawDataRectangle.AffymetrixCelFilereadRawDataRectangle.SpatialReporterreadSequenceDataFramereadSequenceDataFrame.AffymetrixProbeTabFilereadTableInternalreadTableInternal.GenomeInformationreadTableInternal.SnpInformationreadUnitNamesreadUnitNames.AffymetrixNetAffxCsvFilereadUnitsreadUnits.AffymetrixCdfFilereadUnits.AffymetrixCelFilereadUnits.AffymetrixCelSetreadUnits.ChipEffectFilereadUnits.ChipEffectSetreadUnits.CnagCfhFilereadUnits.CnagCfhSetreadUnits.CnChipEffectFilereadUnits.ExonChipEffectFilereadUnits.FirmaFilereadUnits.FirmaSetreadUnits.MultiArrayUnitModelreadUnits.ParameterCelFilereadUnits.ProbeAffinityFilereadUnits.ResidualFilereadUnits.ResidualSetreadUnits.SingleArrayUnitModelreadUnits.SnpChipEffectFilereadUnits.WeightsFilereadUnits.WeightsSetreadUnitsByQuartetsreadUnitsByQuartets.AffymetrixCdfFilerescale.AllelicCrosstalkCalibrationrescaleByAllrescaleByAll.AllelicCrosstalkCalibrationrescaleByAll.ReseqCrosstalkCalibrationrescaleByGroupsrescaleByGroups.AllelicCrosstalkCalibrationReseqCrosstalkCalibrationResidualFileResidualSetrestructrestruct.AffymetrixCdfFileRmaBackgroundCorrectionRmaCnPlmRmaPlmRmaSnpPlmScaleNormalizationScaleNormalization3seq.TransformReportsetAlias.ArrayExplorersetAlias.GenericReportersetAlias.ModelsetAlias.TransformReportsetArrays.ArrayExplorersetBandwidthsetBandwidth.SmoothMultiarrayModelsetCdfsetCdf.AffymetrixCelFilesetCdf.AffymetrixCelSetsetCdf.AffymetrixCnChpFilesetCdf.AffymetrixCnChpSetsetCdf.CnagCfhFilesetCdf.CnagCfhSetsetColorMapssetColorMaps.ArrayExplorersetColorMaps.SpatialReportersetCombineAllelessetCombineAlleles.CnChipEffectSetsetCombineAlleles.CnPlmsetCombineAlleles.CnProbeAffinityFilesetCustomFindCdfsetDecodeFunctionsetDecodeFunction.ParameterCelFilesetEncodeFunctionsetEncodeFunction.ParameterCelFilesetGenomeInformationsetGenomeInformation.AffymetrixCdfFilesetLabel.ModelsetListOfPriorssetListOfPriors.MultiArrayUnitModelsetMergeFunctionsetMergeFunction.ChipEffectGroupMergesetMergeGroupssetMergeGroups.ExonChipEffectSetsetMergeGroups.ExonProbeAffinityFilesetMergeGroups.ExonRmaPlmsetMergeStrandssetMergeStrands.SnpChipEffectSetsetMergeStrands.SnpPlmsetMergeStrands.SnpProbeAffinityFilesetReference.SpatialReportersetRestructorsetRestructor.AffymetrixCdfFilesetSettingssetSettings.PackagesetSnpInformationsetSnpInformation.AffymetrixCdfFilesetTags.ModelsetUnitReadMapsetUnitReadMap.AffymetrixCnChpFilesetup.GenericReportersetupExampleDatasetupExampleData.AromaAffymetrixSingleArrayUnitModelSmoothMultiarrayModelSmoothRmaModelSmoothSaModelsmoothScatterMvsAsmoothScatterMvsA.AffymetrixCelFileSnpChipEffectFileSnpChipEffectGroupMergeSnpChipEffectSetSnpInformationSnpPlmSnpProbeAffinityFileSpatialReporterSpatialRowColumnNormalizationstextChipType.AffymetrixCdfFileTransformtransformAffinetransformAffine.AffymetrixCelFiletransformAffine.AffymetrixCelSetTransformReporttranslateColumnNames.AffymetrixAptSummaryFiletranslateColumnNames.AffymetrixProbeTabFiletranslateColumnNames.AffymetrixTabularFiletranslateFullName.AffymetrixProbeTabFileUflSnpInformationUgpGenomeInformationUnitModelUnitTypeScaleNormalizationupdate.AromaAffymetrixupdate2.AffymetrixCelSetupdateDataFlatupdateDataFlat.ChipEffectFileupdateDataFlat.FirmaFileupdateDataFlat.ResidualFileupdateDataFlat.WeightsFileupdateMatchScoresupdateMatchScores.AromaCellMatchScoreFileupdateParameterupdateParameter.CrlmmParametersFileupdateSampleAnnotationSetupdateSampleAnnotationSet.AffymetrixCelSetupdateSettingsupdateSettings.PackageupdateSetupExplorerFile.ArrayExplorerupdateUnitsupdateUnits.AffymetrixCelFileupdateUnits.ChipEffectFileupdateUnits.ChipEffectSetupdateUnits.FirmaFileupdateUnits.FirmaSetupdateUnits.ParameterCelFileupdateUnits.ProbeAffinityFileupdateUnits.ResidualFileupdateUnits.ResidualSetupdateUnits.WeightsFileupdateUnits.WeightsSetvalidate.AffymetrixCdfFilevalidate.AvgPlmvalidate.MultiArrayUnitModelverify.AffymetrixCsvGenomeInformationverify.AffymetrixTsvFileverify.DChipGenomeInformationverify.DChipSnpInformationverify.GenomeInformationverify.SnpInformationverify.UflSnpInformationverify.UgpGenomeInformationWeightsFileWeightsSetwriteAsFullCelFilewriteAsFullCelFile.ChipEffectFilewriteCdfwriteCdf.AffyGenePDInfowriteCdf.DBPDInfowriteCdf.defaultwriteCdf.PDInfoListwriteCdfByExcludingCellswriteCdfByExcludingCells.AffymetrixCdfFilewriteCNTwriteCNT.SnpChipEffectFilewriteCNT.SnpChipEffectSetwriteImage.AffymetrixCelFilewriteImage.ResidualFilewriteImage.WeightsFilewriteImageCombinedwriteImageCombined.TransformReportwriteImageswriteImages.SpatialReporterwriteImages.TransformReportwriteRegions.profileCGHwriteSgrwriteSgr.AffymetrixCelSetwriteSignalswriteSignals.ProbeLevelTransform3writeWigwriteWig.CnChipEffectSet
Dependencies:aroma.apdaroma.corearoma.lightbase64encBiocManagercodetoolsdigestDNAcopyfutureglobalslistenvMASSmatrixStatsparallellyPSCBSR.cacheR.devicesR.filesetsR.hugeR.methodsS3R.ooR.rspR.utilsRColorBrewer
