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aroma.affymetrix  

Analysis of Large Affymetrix Microarray Data Sets
View on CRAN: Click here


Download and install aroma.affymetrix package within the R console
Install from CRAN:
install.packages("aroma.affymetrix")

Install from Github:
library("remotes")
install_github("cran/aroma.affymetrix")

Install by package version:
library("remotes")
install_version("aroma.affymetrix", "3.2.2")



Attach the package and use:
library("aroma.affymetrix")
Maintained by
Henrik Bengtsson
[Scholar Profile | Author Map]
First Published: 2009-06-29
Latest Update: 2024-02-18
Description:
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.
How to cite:
Henrik Bengtsson (2009). aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets. R package version 3.2.2, https://cran.r-project.org/web/packages/aroma.affymetrix. Accessed 22 Feb. 2025.
Previous versions and publish date:
1.1.1 (2009-06-29 20:32), 1.2.0 (2009-09-10 11:52), 1.3.0 (2009-11-03 12:26), 1.4.0 (2010-01-07 16:41), 1.5.0 (2010-02-23 12:30), 1.6.0 (2010-05-16 18:15), 1.7.0 (2010-07-26 13:49), 1.8.0 (2010-11-08 08:29), 1.9.0 (2011-01-10 15:37), 2.0.0 (2011-02-17 14:07), 2.1.0 (2011-04-09 11:28), 2.1.6 (2011-08-02 08:15), 2.1.8 (2011-08-29 19:37), 2.2.0 (2011-09-03 06:48), 2.3.0 (2011-11-02 18:25), 2.4.0 (2012-01-12 17:32), 2.5.0 (2012-03-26 08:06), 2.6.0 (2012-09-06 07:27), 2.7.0 (2012-11-26 08:51), 2.8.0 (2012-12-22 10:47), 2.9.0 (2013-05-03 08:22), 2.10.0 (2013-08-06 07:39), 2.11.1 (2013-10-18 19:56), 2.12.0 (2014-03-10 00:30), 2.13.0 (2015-01-20 12:41), 2.13.2 (2015-05-27 08:55), 2.14.0 (2015-10-25 08:55), 3.0.0 (2016-01-10 00:00), 3.1.0 (2017-03-24 06:37), 3.1.1 (2018-04-16 20:53), 3.2.0 (2019-06-23 08:00), 3.2.1 (2022-07-18 12:50)
Other packages that cited aroma.affymetrix R package
View aroma.affymetrix citation profile
Other R packages that aroma.affymetrix depends, imports, suggests or enhances
Complete documentation for aroma.affymetrix
Functions, R codes and Examples using the aroma.affymetrix R package
Some associated functions: AbstractProbeSequenceNormalization . AdditiveCovariatesNormalization . AffineCnPlm . AffinePlm . AffineSnpPlm . AffymetrixCdfFile . AffymetrixCelFile . AffymetrixCelSet . AffymetrixCelSetReporter . AffymetrixCelSetTuple . AffymetrixCnChpSet . AffymetrixFile . AffymetrixFileSet . AffymetrixFileSetReporter . AffymetrixPgfFile . AffymetrixProbeTabFile . AlleleSummation . AllelicCrosstalkCalibration . AromaChipTypeAnnotationFile . ArrayExplorer . AvgCnPlm . AvgPlm . AvgSnpPlm . BackgroundCorrection . BaseCountNormalization . BasePositionNormalization . ChipEffectFile . ChipEffectGroupMerge . ChipEffectSet . ChipEffectTransform . CnChipEffectFile . CnChipEffectSet . CnPlm . CnProbeAffinityFile . CnagCfhFile . CnagCfhSet . CrlmmParametersFile . CrlmmParametersSet . DChipCdfBinFile . DChipDcpFile . DChipDcpSet . DChipGenomeInformation . DChipQuantileNormalization . DChipSnpInformation . ExonChipEffectFile . ExonChipEffectSet . ExonProbeAffinityFile . ExonRmaPlm . FirmaFile . FirmaModel . FirmaSet . FragmentEquivalentClassNormalization . FragmentLengthNormalization . GcContentNormalization . GcContentNormalization2 . GcRmaBackgroundCorrection . GenericReporter . GenomeInformation . HetLogAddCnPlm . HetLogAddPlm . HetLogAddSnpPlm . LimmaBackgroundCorrection . LinearModelProbeSequenceNormalization . MatNormalization . MatSmoothing . MbeiCnPlm . MbeiPlm . MbeiSnpPlm . Model . MultiArrayUnitModel . Non-documented_objects . NormExpBackgroundCorrection . OpticalBackgroundCorrection . ParameterCelFile . ParameterCelSet . ProbeAffinityFile . ProbeLevelModel . ProbeLevelTransform . ProbeLevelTransform3 . QualityAssessmentFile . QualityAssessmentModel . QualityAssessmentSet . QuantileNormalization . ReseqCrosstalkCalibration . ResidualFile . ResidualSet . RmaBackgroundCorrection . RmaCnPlm . RmaPlm . RmaSnpPlm . ScaleNormalization . ScaleNormalization3 . SingleArrayUnitModel . SmoothMultiarrayModel . SmoothRmaModel . SnpChipEffectFile . SnpChipEffectGroupMerge . SnpChipEffectSet . SnpInformation . SnpPlm . SnpProbeAffinityFile . SpatialReporter . TransformReport . UgpGenomeInformation . UnitModel . UnitTypeScaleNormalization . WeightsFile . WeightsSet . allocateFromCdf.AffymetrixCelFile . allocateFromCdf.AromaUnitTabularBinaryFile . aroma.affymetrix-package . as.AffymetrixCelSet.AffymetrixCelSet . as.AffymetrixCnChpSet.AffymetrixCnChpSet . as.AffymetrixFileSet.AffymetrixFileSet . as.CnagCfhSet.CnagCfhSet . as.DChipDcpSet.DChipDcpSet . as.character.AffymetrixCelSet . as.character.AffymetrixCnChpSet . as.character.CnagCfhSet . as.character.DChipDcpSet . averageQuantile.AffymetrixCelSet . bpmapCluster2Cdf . byChipType.AromaChipTypeAnnotationFile . byChipType.DChipGenomeInformation . byChipType.DChipSnpInformation . byChipType.GenomeInformation . byChipType.SnpInformation . byChipType.UgpGenomeInformation . byPath.AffymetrixFileSet . calculateBaseline.ChipEffectSet . calculateParametersGsb.AffymetrixCelSet . calculateResidualSet.FirmaModel . clearData.AffymetrixCelFile . compare.AffymetrixCdfFile . computeAffinities.AffymetrixCdfFile . convert.AffymetrixCdfFile . convertUnits.AffymetrixCdfFile . createExonByTranscriptCdf.AffymetrixCdfFile . createFrom.AffymetrixCelFile . createMonocellCdf.AffymetrixCdfFile . createUniqueCdf.AffymetrixCdfFile . doCRMAv1 . doCRMAv2 . doFIRMA . doGCRMA . doRMA . extractAffyBatch.AffymetrixCelSet . extractDataFrame.ParameterCelSet . extractExpressionSet.ChipEffectSet . extractFeatureSet.AffymetrixCelSet . extractMatrix.AffymetrixCelSet . extractMatrix.ParameterCelSet . findByChipType.AffymetrixCdfFile . findByChipType.AffymetrixPgfFile . findByChipType.AromaChipTypeAnnotationFile . findUnitsTodo.FirmaModel . findUnitsTodo.ProbeLevelModel . findUnitsTodo.UnitModel . fit.FirmaModel . fit.Model . fit.ProbeLevelModel . fit.SingleArrayUnitModel . fit.SmoothMultiarrayModel . fitQuantileNormFcn.AffymetrixCelFile . fromCdf.GenomeInformation . fromCdf.SnpInformation . fromDataFile.ChipEffectFile . fromFile.AffymetrixCdfFile . fromFile.AffymetrixCelFile . fromFile.AffymetrixPgfFile . fromFile.AromaChipTypeAnnotationFile . fromFile.CnagCfhFile . getAM.ChipEffectFile . getAM.ChipEffectSet . getAlias.GenericReporter . getAlias.Model . getAlleleCellPairs.AffymetrixCdfFile . getAlleleProbePairs.AffymetrixCdfFile . getAlleleProbePairs3.AffymetrixCdfFile . getAverageFile.AffymetrixCelSet . getAverageFile.CnagCfhSet . getBaseline.ChipEffectSet . getCdf.AffymetrixCelFile . getCdf.AffymetrixCelSet . getCdf.CnagCfhFile . getCdf.CnagCfhSet . getCdf.Model . getCellIndices.AffymetrixCdfFile . getCellIndices.ChipEffectFile . getCellIndices.CnChipEffectFile . getCellIndices.CnProbeAffinityFile . getCellIndices.ExonChipEffectFile . getCellIndices.ExonProbeAffinityFile . getCellIndices.FirmaFile . getCellIndices.ProbeAffinityFile . getCellIndices.ResidualFile . getCellIndices.SnpChipEffectFile . getCellIndices.SnpProbeAffinityFile . getCellIndices.UnitModel . getCellIndices.WeightsFile . getChipEffectSet.AlleleSummation . getChipEffectSet.ProbeLevelModel . getChipType.AffymetrixCelFile . getChipType.AffymetrixCelSet . getChipType.CnagCfhFile . getChipType.GenomeInformation . getChipType.SnpInformation . getCnNames.AffymetrixCdfFile . getData.GenomeInformation . getData.SnpInformation . getDataSet.AffymetrixCelSetReporter . getDataSet.ArrayExplorer . getDataSet.Model . getFirmaSet.FirmaModel . getFitUnitGroupFunction.AffinePlm . getFitUnitGroupFunction.AvgPlm . getFitUnitGroupFunction.ExonRmaPlm . getFitUnitGroupFunction.FirmaModel . getFitUnitGroupFunction.HetLogAddPlm . getFitUnitGroupFunction.MbeiPlm . getFitUnitGroupFunction.MultiArrayUnitModel . getFitUnitGroupFunction.RmaPlm . getFitUnitGroupFunction.SingleArrayUnitModel . getFullName.Model . getFullName.TransformReport . getGenomeInformation.AffymetrixCdfFile . getHeader.AffymetrixCdfFile . getHeader.AffymetrixCelFile . getHeader.AffymetrixPgfFile . getHeader.AromaChipTypeAnnotationFile . getHeader.CnagCfhFile . getImage.AffymetrixCelFile . getInputDataSet.TransformReport . getIntensities.AffymetrixCelSet . getName.GenericReporter . getName.Model . getName.TransformReport . getOutputDataSet.Transform . getOutputDataSet.TransformReport . getPath.Model . getPath.TransformReport . getPositions.GenomeInformation . getProbeAffinityFile.ProbeLevelModel . getResiduals.QualityAssessmentModel . getRootPath.Model . getSnpNames.AffymetrixCdfFile . getTags.GenericReporter . getTags.Model . getTags.TransformReport . getTimestamp.AffymetrixCelFile . getUnitGroupCellMap.ChipEffectFile . getUnitIndices.GenomeInformation . getUnitIntensities.AffymetrixCelSet . getUnitNames.AffymetrixCdfFile . getUnitNames.AffymetrixPgfFile . getUnitTypes.AffymetrixCdfFile . getWeights.QualityAssessmentModel . getXAM.ChipEffectFile . getXAM.ChipEffectSet . groupUnitsByDimension.AffymetrixCdfFile . image270.AffymetrixCelFile . importFromApt.CnChipEffectSet . importFromDChip.AffymetrixCelSet . importFromDChip.CnChipEffectSet . isDuplicated.AffymetrixCelSet . isDuplicated.CnagCfhSet . isPm.AffymetrixCdfFile . isResequenceChip.AffymetrixCdfFile . isSnpChip.AffymetrixCdfFile . justRMA . nbrOfArrays.AffymetrixCelSet . nbrOfGroupsPerUnit.AffymetrixCdfFile . nbrOfSnps.AffymetrixCdfFile . normalizeQuantile.AffymetrixCelFile . normalizeQuantile.AffymetrixCelSet . pdInfo2Cdf . plotBoxplotStats.list . plotDensity.AffymetrixCelFile . plotDensity.AffymetrixCelSet . plotDensity.GenomeInformation . plotImage.AffymetrixCelFile . plotMvsA.AffymetrixCelFile . plotMvsX.AffymetrixCelFile . process.AbstractProbeSequenceNormalization . process.AdditiveCovariatesNormalization . process.AllelicCrosstalkCalibration . process.ArrayExplorer . process.BackgroundCorrection . process.ChipEffectGroupMerge . process.DChipQuantileNormalization . process.FragmentEquivalentClassNormalization . process.FragmentLengthNormalization . process.GcContentNormalization . process.GcRmaBackgroundCorrection . process.GenericReporter . process.LimmaBackgroundCorrection . process.MatNormalization . process.MatSmoothing . process.OpticalBackgroundCorrection . process.QuantileNormalization . process.ReseqCrosstalkCalibration . process.RmaBackgroundCorrection . process.ScaleNormalization . process.ScaleNormalization3 . process.SpatialReporter . process.UnitTypeScaleNormalization . randomSeed . readRawData.AffymetrixCelFile . readUnits.AffymetrixCdfFile . readUnits.AffymetrixCelFile . readUnits.CnagCfhFile . readUnits.MultiArrayUnitModel . readUnits.SingleArrayUnitModel . readUnitsByQuartets.AffymetrixCdfFile . setAlias.GenericReporter . setAlias.Model . setArrays.ArrayExplorer . setCdf.AffymetrixCelFile . setCdf.AffymetrixCelSet . setCdf.CnagCfhFile . setCdf.CnagCfhSet . setRestructor.AffymetrixCdfFile . setTags.Model . setupExampleData.AromaAffymetrix . setupExampleData . smoothScatterMvsA.AffymetrixCelFile . updateUnits.AffymetrixCelFile . verify.GenomeInformation . verify.SnpInformation . writeCdf.AffyGenePDInfo . writeImage.AffymetrixCelFile . 
Some associated R codes: 000.R . 006.fixVarArgs.R . 009.setup.R . 021.dynamic_imports.R . 999.AromaAffymetrix.R . 999.DEPRECATED.R . 999.NonDocumentedObjects.R . 999.package.R . ASCRMAv2.R . AbstractProbeSequenceNormalization.R . AdditiveCovariatesNormalization.R . AffineCnPlm.R . AffinePlm.R . AffineSnpPlm.R . AffyGenePDInfo.writeCdf.R . AffymetrixAptSummaryFile.R . AffymetrixCdfFile.COUNTS.R . AffymetrixCdfFile.MONOCELL.R . AffymetrixCdfFile.PLOT.R . AffymetrixCdfFile.R . AffymetrixCdfFile.SNPs.R . AffymetrixCdfFile.UNIQUE.R . AffymetrixCdfFile.computeAffinities.R . AffymetrixCdfFile.getAlleleCellPairs.R . AffymetrixCdfFile.getAlleleProbePairs.R . AffymetrixCdfFile.getAlleleProbePairs2.R . AffymetrixCdfFile.getAlleleProbePairs3.R . AffymetrixCdfFile.getCellQuartets.R . AffymetrixCdfFile.getProbeSequenceData.R . AffymetrixCdfFile.getSubsetOfCellIndices.R . AffymetrixCdfFile.getSubsetOfUnits.R . AffymetrixCdfFile.getUnitGroupCellMap.R . AffymetrixCdfFile.getUnitGroupNamesFromUgcMap.R . AffymetrixCdfFile.groupUnitsByDimension.R . AffymetrixCdfFile.readDataFrame.R . AffymetrixCdfFile.writeCdfByExcludingCells.R . AffymetrixCelFile.BG.R . AffymetrixCelFile.PLOT.R . AffymetrixCelFile.R . AffymetrixCelFile.allocateFromCdf.R . AffymetrixCelFile.createFrom.R . AffymetrixCelFile.extractMatrix.R . AffymetrixCelFile.fitQuantileNormFcn.R . AffymetrixCelFile.normalizeAffine.R . AffymetrixCelFile.normalizeQuantile.R . AffymetrixCelSet.BG.R . AffymetrixCelSet.NORM.R . AffymetrixCelSet.PLOT.R . AffymetrixCelSet.R . AffymetrixCelSet.convertToUnique.R . AffymetrixCelSet.extractAffyBatch.R . AffymetrixCelSet.extractFeatureSet.R . AffymetrixCelSet.extractMatrix.R . AffymetrixCelSet.getAverageFile.R . AffymetrixCelSet.importFromDChip.R . AffymetrixCelSet.justSNPRMA.R . AffymetrixCelSet.writeSgr.R . AffymetrixCelSetReporter.R . AffymetrixCelSetTuple.R . AffymetrixCnChpFile.R . AffymetrixCnChpSet.R . AffymetrixCnChpSet.extras.R . AffymetrixCsvFile.R . AffymetrixCsvGenomeInformation.R . AffymetrixFile.R . AffymetrixFileSet.R . AffymetrixFileSet.getIdentifier.R . AffymetrixFileSetReporter.R . AffymetrixNetAffxCsvFile.R . AffymetrixNetAffxCsvFile.XTRS.R . AffymetrixPgfFile.R . AffymetrixPlatform.R . AffymetrixProbeTabFile.R . AffymetrixTabularFile.R . AffymetrixTsvFile.R . AlleleSummation.R . AllelicCrosstalkCalibration.PLOT.R . AllelicCrosstalkCalibration.R . AllelicCrosstalkCalibration.getSetsOfProbes.R . AromaCellCpgFile.AFFX.R . AromaCellMatchScoreFile.AFFX.R . AromaCellMatchScoreFile.R . AromaCellMatchScoreFile.importFromBpmap.R . AromaCellPositionFile.AFFX.R . AromaCellSequenceFile.AFFX.R . AromaCellSequenceFile.importFromBpmap.R . AromaChipTypeAnnotationFile.R . AromaPipeline.R . AromaUfcFile.R . AromaUflFile.AFFX.R . AromaUgpFile.AFFX.R . AromaUnitGcContentFile.AFFX.R . AromaUnitTabularBinaryFile.AFFX.PLOT.R . AromaUnitTabularBinaryFile.AFFX.R . ArrayExplorer.R . AvgCnPlm.R . AvgPlm.R . AvgSnpPlm.R . BackgroundCorrection.R . BaseCountNormalization.R . BasePositionNormalization.R . BasePositionNormalization.getFit.R . ChipEffectFile.R . ChipEffectFile.TOFULL.R . ChipEffectFile.extractTheta.R . ChipEffectFile.fromDataFile.R . ChipEffectFile.getUnitGroupCellMatrixMap.R . ChipEffectFile.xam.R . ChipEffectGroupMerge.R . ChipEffectNnn.extractChromosomalDataFrame.R . ChipEffectSet.PLOT.R . ChipEffectSet.R . ChipEffectSet.STATS.R . ChipEffectSet.TOFULL.R . ChipEffectSet.calculateBaseline.R . ChipEffectSet.extractExpressionSet.R . ChipEffectSet.extractTheta.R . ChipEffectSet.getBaseline.R . ChipEffectSet.xam.R . ChipEffectSetTuple.R . ChipEffectTransform.R . ChromosomalModel.AFFX.R . ChromosomalModel.getPositionChipTypeUnit.R . ChromosomalModel.getXTheta.R . CnChipEffectFile.R . CnChipEffectFile.exportAromaSignalBinaryFileList.R . CnChipEffectSet.R . CnChipEffectSet.importFromApt.R . CnChipEffectSet.importFromDChip.R . CnChipEffectSet.writeWig.R . CnChipEffectSetTuple.R . CnPlm.R . CnProbeAffinityFile.R . CnagCfhFile.R . CnagCfhSet.R . CopyNumberChromosomalModel.applyCCF.R . CopyNumberSegmentationModel.migrateTool.R . CrlmmModel.EXT.R . CrlmmModel.R . CrlmmParametersFile.R . CrlmmParametersSet.R . DChipCdfBinFile.R . DChipCdfBinFile.mapToUnitNamesFile.R . DChipDcpFile.R . DChipDcpSet.R . DChipDcpSet.extras.R . DChipGenomeInformation.R . DChipQuantileNormalization.R . DChipSnpInformation.R . ExonChipEffectFile.R . ExonChipEffectSet.R . ExonProbeAffinityFile.R . ExonRmaPlm.R . ExonRmaPlm.calculateWeights.R . FirmaFile.R . FirmaModel.R . FirmaSet.R . FragmentEquivalentClassNormalization.R . FragmentLengthNormalization.R . GcContentNormalization.R . GcContentNormalization2.R . GcContentNormalization2.plotCovariateEffects.R . GcRmaBackgroundCorrection.R . GenericReporter.R . GenomeInformation.AFFX.R . GenomeInformation.R . HetLogAddCnPlm.R . HetLogAddPlm.R . HetLogAddSnpPlm.R . LimmaBackgroundCorrection.R . LinearModelProbeSequenceNormalization.R . MatNormalization.R . MatSmoothing.R . MbeiCnPlm.R . MbeiPlm.R . MbeiSnpPlm.R . Model.R . MultiArrayUnitModel.R . NormExpBackgroundCorrection.R . OpticalBackgroundCorrection.R . Package.XTRA.R . ParameterCelFile.R . ParameterCelFile.extractNnn.R . ParameterCelSet.R . ProbeAffinityFile.R . ProbeLevelModel.R . ProbeLevelModel.calculateResiduals.R . ProbeLevelModel.calculateWeights.R . ProbeLevelModel.fit.R . ProbeLevelTransform.R . ProbeLevelTransform3.R . QualityAssessmentFile.R . QualityAssessmentModel.R . QualityAssessmentSet.R . QuantileNormalization.R . QuantileNormalization.xtra.R . ReseqCrosstalkCalibration.R . ResidualFile.R . ResidualSet.R . RmaBackgroundCorrection.R . RmaCnPlm.R . RmaPlm.R . RmaSnpPlm.R . ScaleNormalization.R . ScaleNormalization3.R . SingleArrayUnitModel.R . SingleArrayUnitModel.fit.R . SmoothMultiarrayModel.R . SmoothMultiarrayModel.fit.R . SmoothRmaModel.R . SmoothSaModel.R . SnpChipEffectFile.R . SnpChipEffectFile.exportTotalAndFracB.R . SnpChipEffectFile.extractTotalAndFracB.R . SnpChipEffectGroupMerge.R . SnpChipEffectNnn.extractCNT.R . SnpChipEffectNnn.writeCNT.R . SnpChipEffectSet.R . SnpChipEffectSet.exportTotalAndFracB.R . SnpChipEffectSet.extractAlleleSet.R . SnpChipEffectSet.extractSnpCnvQSet.R . SnpChipEffectSet.extractSnpQSet.R . SnpChipEffectSet.extractTotalAndFreqB.R . SnpCnvQSet.extractTheta.R . SnpInformation.R . SnpPlm.R . SnpProbeAffinityFile.R . SnpQSet.extractTheta.R . SpatialReporter.R . SpatialRowColumnNormalization.R . Transform.R . TransformReport.R . UflSnpInformation.R . UgpGenomeInformation.R . UnitModel.R . UnitModel.fitCnProbes.R . UnitTypeScaleNormalization.R . WeightsFile.R . WeightsSet.R . bpmapCluster2Cdf.R . createExonByTranscriptCdf.R . doCRMAv1.R . doCRMAv2.R . doFIRMA.R . doGCRMA.R . doRMA.R . dropCellsFromCdfList.R . env2Cdf.R . findByCdf2.R . fitPlasqUnit.R . getPlasqTypes.R . isUnitGroupCellMap.R . justRMA.R . pdInfo2Cdf.R . plotBoxplotStats.list.R . profileCGH.getRegions.R . profileCGH.writeRegions.R . randomSeed.R . readCdfGroupStrands.R . readCfhHeader.R . readCfhUnits.R . readCfnHeader.R . readCfnUnits.R . setCustomFindCdf.R . setupExampleData.R . zzz.R .  Full aroma.affymetrix package functions and examples
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