Files in HenrikBengtsson/aroma.affymetrix

Analysis of Large Affymetrix Microarray Data Sets

CONDUCT.md INSTALL.md OVERVIEW.md R/000.R R/006.fixVarArgs.R R/009.setup.R R/021.dynamic_imports.R R/999.AromaAffymetrix.R R/999.DEPRECATED.R R/999.NonDocumentedObjects.R R/999.package.R R/ASCRMAv2.R R/AbstractProbeSequenceNormalization.R R/AdditiveCovariatesNormalization.R R/AffineCnPlm.R R/AffinePlm.R R/AffineSnpPlm.R R/AffyGenePDInfo.writeCdf.R R/AffymetrixAptSummaryFile.R R/AffymetrixCdfFile.COUNTS.R R/AffymetrixCdfFile.MONOCELL.R R/AffymetrixCdfFile.PLOT.R R/AffymetrixCdfFile.R R/AffymetrixCdfFile.SNPs.R R/AffymetrixCdfFile.UNIQUE.R R/AffymetrixCdfFile.computeAffinities.R R/AffymetrixCdfFile.getAlleleCellPairs.R R/AffymetrixCdfFile.getAlleleProbePairs.R R/AffymetrixCdfFile.getAlleleProbePairs2.R R/AffymetrixCdfFile.getAlleleProbePairs3.R R/AffymetrixCdfFile.getCellQuartets.R R/AffymetrixCdfFile.getProbeSequenceData.R R/AffymetrixCdfFile.getSubsetOfCellIndices.R R/AffymetrixCdfFile.getSubsetOfUnits.R R/AffymetrixCdfFile.getUnitGroupCellMap.R R/AffymetrixCdfFile.getUnitGroupNamesFromUgcMap.R R/AffymetrixCdfFile.groupUnitsByDimension.R R/AffymetrixCdfFile.readDataFrame.R R/AffymetrixCdfFile.writeCdfByExcludingCells.R R/AffymetrixCelFile.PLOT.R R/AffymetrixCelFile.R R/AffymetrixCelFile.allocateFromCdf.R R/AffymetrixCelFile.createFrom.R R/AffymetrixCelFile.extractMatrix.R R/AffymetrixCelFile.fitQuantileNormFcn.R R/AffymetrixCelFile.normalizeAffine.R R/AffymetrixCelFile.normalizeQuantile.R R/AffymetrixCelSet.BG.R R/AffymetrixCelSet.NORM.R R/AffymetrixCelSet.PLOT.R R/AffymetrixCelSet.R R/AffymetrixCelSet.convertToUnique.R R/AffymetrixCelSet.extractAffyBatch.R R/AffymetrixCelSet.extractFeatureSet.R R/AffymetrixCelSet.extractMatrix.R R/AffymetrixCelSet.getAverageFile.R R/AffymetrixCelSet.importFromDChip.R R/AffymetrixCelSet.justSNPRMA.R R/AffymetrixCelSet.writeSgr.R R/AffymetrixCelSetReporter.R R/AffymetrixCelSetTuple.R R/AffymetrixCnChpFile.R R/AffymetrixCnChpSet.R R/AffymetrixCnChpSet.extras.R R/AffymetrixCsvFile.R R/AffymetrixCsvGenomeInformation.R R/AffymetrixFile.R R/AffymetrixFileSet.R R/AffymetrixFileSet.getIdentifier.R R/AffymetrixFileSetReporter.R R/AffymetrixNetAffxCsvFile.R R/AffymetrixNetAffxCsvFile.XTRS.R R/AffymetrixPgfFile.R R/AffymetrixPlatform.R R/AffymetrixProbeTabFile.R R/AffymetrixTabularFile.R R/AffymetrixTsvFile.R R/AlleleSummation.R R/AllelicCrosstalkCalibration.PLOT.R R/AllelicCrosstalkCalibration.R R/AllelicCrosstalkCalibration.getSetsOfProbes.R R/AromaCellCpgFile.AFFX.R R/AromaCellMatchScoreFile.AFFX.R R/AromaCellMatchScoreFile.R R/AromaCellMatchScoreFile.importFromBpmap.R R/AromaCellPositionFile.AFFX.R R/AromaCellSequenceFile.AFFX.R R/AromaCellSequenceFile.importFromBpmap.R R/AromaChipTypeAnnotationFile.R R/AromaPipeline.R R/AromaUfcFile.R R/AromaUflFile.AFFX.R R/AromaUgpFile.AFFX.R R/AromaUnitGcContentFile.AFFX.R R/AromaUnitTabularBinaryFile.AFFX.PLOT.R R/AromaUnitTabularBinaryFile.AFFX.R R/ArrayExplorer.R R/AvgCnPlm.R R/AvgPlm.R R/AvgSnpPlm.R R/BackgroundCorrection.R R/BaseCountNormalization.R R/BasePositionNormalization.R R/BasePositionNormalization.getFit.R R/ChipEffectFile.R R/ChipEffectFile.TOFULL.R R/ChipEffectFile.extractTheta.R R/ChipEffectFile.fromDataFile.R R/ChipEffectFile.getUnitGroupCellMatrixMap.R R/ChipEffectFile.xam.R R/ChipEffectGroupMerge.R R/ChipEffectNnn.extractChromosomalDataFrame.R R/ChipEffectSet.PLOT.R R/ChipEffectSet.R R/ChipEffectSet.STATS.R R/ChipEffectSet.TOFULL.R R/ChipEffectSet.calculateBaseline.R R/ChipEffectSet.extractExpressionSet.R R/ChipEffectSet.extractTheta.R R/ChipEffectSet.getBaseline.R R/ChipEffectSet.xam.R R/ChipEffectSetTuple.R R/ChipEffectTransform.R R/ChromosomalModel.AFFX.R R/ChromosomalModel.getPositionChipTypeUnit.R R/ChromosomalModel.getXTheta.R R/CnChipEffectFile.R R/CnChipEffectFile.exportAromaSignalBinaryFileList.R R/CnChipEffectSet.R R/CnChipEffectSet.importFromApt.R R/CnChipEffectSet.importFromDChip.R R/CnChipEffectSet.writeWig.R R/CnChipEffectSetTuple.R R/CnPlm.R R/CnProbeAffinityFile.R R/CnagCfhFile.R R/CnagCfhSet.R R/CopyNumberChromosomalModel.applyCCF.R R/CopyNumberSegmentationModel.migrateTool.R R/CrlmmModel.EXT.R R/CrlmmModel.R R/CrlmmParametersFile.R R/CrlmmParametersSet.R R/DChipCdfBinFile.R R/DChipCdfBinFile.mapToUnitNamesFile.R R/DChipDcpFile.R R/DChipDcpSet.R R/DChipDcpSet.extras.R R/DChipGenomeInformation.R R/DChipQuantileNormalization.R R/DChipSnpInformation.R R/ExonChipEffectFile.R R/ExonChipEffectSet.R R/ExonProbeAffinityFile.R R/ExonRmaPlm.R R/ExonRmaPlm.calculateWeights.R R/FirmaFile.R R/FirmaModel.R R/FirmaSet.R R/FragmentEquivalentClassNormalization.R R/FragmentLengthNormalization.R R/GcContentNormalization.R R/GcContentNormalization2.R R/GcContentNormalization2.plotCovariateEffects.R R/GcRmaBackgroundCorrection.R R/GenericReporter.R R/GenomeInformation.AFFX.R R/GenomeInformation.R R/HetLogAddCnPlm.R R/HetLogAddPlm.R R/HetLogAddSnpPlm.R R/LimmaBackgroundCorrection.R R/LinearModelProbeSequenceNormalization.R R/MatNormalization.R R/MatSmoothing.R R/MbeiCnPlm.R R/MbeiPlm.R R/MbeiSnpPlm.R R/Model.R R/MultiArrayUnitModel.R R/NormExpBackgroundCorrection.R R/OpticalBackgroundCorrection.R R/Package.XTRA.R R/ParameterCelFile.R R/ParameterCelFile.extractNnn.R R/ParameterCelSet.R R/ProbeAffinityFile.R R/ProbeLevelModel.R R/ProbeLevelModel.calculateResiduals.R R/ProbeLevelModel.calculateWeights.R R/ProbeLevelModel.fit.R R/ProbeLevelTransform.R R/ProbeLevelTransform3.R R/QualityAssessmentFile.R R/QualityAssessmentModel.R R/QualityAssessmentSet.R R/QuantileNormalization.R R/QuantileNormalization.xtra.R R/ReseqCrosstalkCalibration.R R/ResidualFile.R R/ResidualSet.R R/RmaBackgroundCorrection.R R/RmaCnPlm.R R/RmaPlm.R R/RmaSnpPlm.R R/ScaleNormalization.R R/ScaleNormalization3.R R/SingleArrayUnitModel.R R/SingleArrayUnitModel.fit.R R/SmoothMultiarrayModel.R R/SmoothMultiarrayModel.fit.R R/SmoothRmaModel.R R/SmoothSaModel.R R/SnpChipEffectFile.R R/SnpChipEffectFile.exportTotalAndFracB.R R/SnpChipEffectFile.extractTotalAndFracB.R R/SnpChipEffectGroupMerge.R R/SnpChipEffectNnn.extractCNT.R R/SnpChipEffectNnn.writeCNT.R R/SnpChipEffectSet.R R/SnpChipEffectSet.exportTotalAndFracB.R R/SnpChipEffectSet.extractAlleleSet.R R/SnpChipEffectSet.extractSnpCnvQSet.R R/SnpChipEffectSet.extractSnpQSet.R R/SnpChipEffectSet.extractTotalAndFreqB.R R/SnpCnvQSet.extractTheta.R R/SnpInformation.R R/SnpPlm.R R/SnpProbeAffinityFile.R R/SnpQSet.extractTheta.R R/SpatialReporter.R R/SpatialRowColumnNormalization.R R/Transform.R R/TransformReport.R R/UflSnpInformation.R R/UgpGenomeInformation.R R/UnitModel.R R/UnitModel.fitCnProbes.R R/UnitTypeScaleNormalization.R R/WeightsFile.R R/WeightsSet.R R/bpmapCluster2Cdf.R R/createExonByTranscriptCdf.R R/doCRMAv1.R R/doCRMAv2.R R/doFIRMA.R R/doGCRMA.R R/doRMA.R R/dropCellsFromCdfList.R R/env2Cdf.R R/findByCdf2.R R/fitPlasqUnit.R R/getPlasqTypes.R R/isUnitGroupCellMap.R R/justRMA.R R/pdInfo2Cdf.R R/plotBoxplotStats.list.R R/profileCGH.getRegions.R R/profileCGH.writeRegions.R R/randomSeed.R R/readCdfGroupStrands.R R/readCfhHeader.R R/readCfhUnits.R R/readCfnHeader.R R/readCfnUnits.R R/setCustomFindCdf.R R/setupExampleData.R R/zzz.R README.md cran-comments.md inst/buildScripts/chipTypes/Canine_2/Canine_2,ACS.R inst/buildScripts/chipTypes/CytoScanHD_Array/CytoScanHD_Array,ACS.R inst/buildScripts/chipTypes/CytoScanHD_Array/na32/CytoScanHD_Array,UFL.R inst/buildScripts/chipTypes/CytoScanHD_Array/na32/CytoScanHD_Array,UGP.R inst/buildScripts/chipTypes/Cytogenetics_Array/Cytogenetics_Array,ACS.R inst/buildScripts/chipTypes/Cytogenetics_Array/na28/Cytogenetics_Array,UGP,na28.R inst/buildScripts/chipTypes/DogSty06m520431/DogSty06m520431,ACS.R inst/buildScripts/chipTypes/GenomeWideSNP_5/na25/GenomeWideSNP_5,UFL,na25,GWS6.R inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GWS5,default,UGP+UFL,na26.R inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GenomeWideSNP_5,UFL,na26,GWS6.R inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GenomeWideSNP_5,UFL,na26.R inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GenomeWideSNP_5,UGP,na26.R inst/buildScripts/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,UFL.R inst/buildScripts/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,UGP.R inst/buildScripts/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,default,UGP+UFL.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na25/GenomeWideSNP_6,UFL,na25.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na26/GWS6,default,UGP+UFL,na26.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na26/GenomeWideSNP_6,UFL,na26.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na26/GenomeWideSNP_6,UGP,na26.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1/GWS6,default,UGP+UFL,na27.1.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1/GenomeWideSNP_6,UFL,na27.1.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1/GenomeWideSNP_6,UGP,na27.1.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na27/GenomeWideSNP_6,UGC,na27.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na30/GenomeWideSNP_6,UFL,na30.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na30/GenomeWideSNP_6,UGP,na30.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na31/GenomeWideSNP_6,UFL.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na31/GenomeWideSNP_6,UGP.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na31/GenomeWideSNP_6,default,UGP+UFL.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na32/GenomeWideSNP_6,UFL.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na32/GenomeWideSNP_6,UGP.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na32/GenomeWideSNP_6,default,UGP+UFL.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na33/GenomeWideSNP_6,UFL.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na33/GenomeWideSNP_6,UGP.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na33/GenomeWideSNP_6,default,UGP+UFL.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na35/1.GenomeWideSNP_6,UGP.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na35/2.GenomeWideSNP_6,UFL.R inst/buildScripts/chipTypes/GenomeWideSNP_6/na35/3.GenomeWideSNP_6,default.R inst/buildScripts/chipTypes/HG-Focus/HG-Focus,ACS.R inst/buildScripts/chipTypes/HG-U133A/HG-U133A,ACS.R inst/buildScripts/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2,ACS.R inst/buildScripts/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2,CDF,exonByTranscript.R inst/buildScripts/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,ACS.R inst/buildScripts/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,NetAffx.R inst/buildScripts/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650,ACS.R inst/buildScripts/chipTypes/MOUSEDIVm520650/na30/MOUSEDIVm520650,UFL,na30.R inst/buildScripts/chipTypes/MOUSEDIVm520650/na30/MOUSEDIVm520650,UGP,na30.R inst/buildScripts/chipTypes/Mapping10K_Xba131/Mapping10K_Xba131,ACS.R inst/buildScripts/chipTypes/Mapping10K_Xba131/na26/Mapping10K_Xba131,UFL,na26.R inst/buildScripts/chipTypes/Mapping10K_Xba131/na26/Mapping10K_Xba131,UGP,na26.R inst/buildScripts/chipTypes/Mapping10K_Xba142/Mapping10K_Xba142,ACS.R inst/buildScripts/chipTypes/Mapping10K_Xba142/na26/Mapping10K_Xba142,UFL,na26.R inst/buildScripts/chipTypes/Mapping10K_Xba142/na26/Mapping10K_Xba142,UGP,na26.R inst/buildScripts/chipTypes/Mapping250K_Nsp/na26/Mapping250K_Nsp,UFL,na26.R inst/buildScripts/chipTypes/Mapping250K_Nsp/na26/Mapping250K_Nsp,UGP,na26.R inst/buildScripts/chipTypes/Mapping250K_Nsp/na28/Mapping250K_Nsp,UGC,na28.R inst/buildScripts/chipTypes/Mapping250K_Nsp/na31/Mapping250K_Nsp,UFL,na31.R inst/buildScripts/chipTypes/Mapping250K_Nsp/na31/Mapping250K_Nsp,UGP,na31.R inst/buildScripts/chipTypes/Mapping250K_Sty/na26/Mapping250K_Sty,UFL,na26.R inst/buildScripts/chipTypes/Mapping250K_Sty/na26/Mapping250K_Sty,UGP,na26.R inst/buildScripts/chipTypes/Mapping250K_Sty/na28/Mapping250K_Sty,UGC,na28.R inst/buildScripts/chipTypes/Mapping250K_Sty/na31/Mapping250K_Sty,UFL,na31.R inst/buildScripts/chipTypes/Mapping250K_Sty/na31/Mapping250K_Sty,UGP,na31.R inst/buildScripts/chipTypes/Mapping50K_Hind240/Mapping50K_Hind240,UFL.R inst/buildScripts/chipTypes/Mapping50K_Hind240/Mapping50K_Xba240,UGP.R inst/buildScripts/chipTypes/Mapping50K_Hind240/na26/Mapping50K_Hind240,UFL,na26.R inst/buildScripts/chipTypes/Mapping50K_Hind240/na26/Mapping50K_Hind240,UGP,na26.R inst/buildScripts/chipTypes/Mapping50K_Xba240/Mapping50K_Xba240,ACS.R inst/buildScripts/chipTypes/Mapping50K_Xba240/Mapping50K_Xba240,UFL.R inst/buildScripts/chipTypes/Mapping50K_Xba240/Mapping50K_Xba240,UGP.R inst/buildScripts/chipTypes/Mapping50K_Xba240/na26/Mapping50K_Xba240,UFL,na26.R inst/buildScripts/chipTypes/Mapping50K_Xba240/na26/Mapping50K_Xba240,UGP,na26.R inst/buildScripts/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1,ACP.R inst/buildScripts/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1,ACS.R inst/buildScripts/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1,UGP.R inst/downloadScripts/chipTypes/Mapping50K_Hind240,Xba240/HapMap,testSet,100K.R inst/testScripts/R/downloadUtils.R inst/testScripts/R/installUtils.R inst/testScripts/R/launchUtils.R inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty/01a.downloadAnnotationData.R inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty/01b.downloadRawData.R inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty/01c.installPackages.R inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty/11.doASCRMAv2,TCNs,500K.R inst/testScripts/addons/chipTypes/Mapping250K_Nsp/01a.downloadAnnotationData.R inst/testScripts/addons/chipTypes/Mapping250K_Nsp/01b.downloadRawData.R inst/testScripts/addons/chipTypes/Mapping250K_Nsp/01c.installPackages.R inst/testScripts/addons/chipTypes/Mapping250K_Nsp/21.doASCRMAv2,CalMaTe.R inst/testScripts/addons/chipTypes/Mapping250K_Nsp/31.doASCRMAv2,PSCBS.R inst/testScripts/addons/chipTypes/Mapping50K_Hind240/01a.downloadAnnotationData.R inst/testScripts/addons/chipTypes/Mapping50K_Hind240/01b.downloadRawData.R inst/testScripts/addons/chipTypes/Mapping50K_Hind240/01c.installPackages.R inst/testScripts/addons/chipTypes/Mapping50K_Hind240/21.doACNE,seg.R inst/testScripts/annotation/chipTypes/GenomeWideSNP_6/01a.downloadAnnotationData.R inst/testScripts/annotation/chipTypes/GenomeWideSNP_6/11.UFL.R inst/testScripts/annotation/chipTypes/GenomeWideSNP_6/21.UGP.R inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/21.TCN,500K.R inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/31.ASCN,paired.R inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/31.ASCN.R inst/testScripts/complete/dataSets/GSE12702/01a.downloadAnnotationData.R inst/testScripts/complete/dataSets/GSE12702/01b.downloadRawData.R inst/testScripts/complete/dataSets/GSE12702/01c.installPackages.R inst/testScripts/complete/dataSets/GSE12702/11.doASCRMAv2,Nsp.R inst/testScripts/complete/dataSets/GSE12702/11.doASCRMAv2,Sty.R inst/testScripts/complete/dataSets/GSE12702/22.doASCRMAv2,CalMaTe,Nsp.R inst/testScripts/complete/dataSets/GSE12702/22.doASCRMAv2,CalMaTe,Sty.R inst/testScripts/complete/dataSets/GSE12702/31.doASCRMAv2,PairedPSCBS,Nsp.R inst/testScripts/complete/dataSets/GSE12702/31.doASCRMAv2,PairedPSCBS,Sty.R inst/testScripts/complete/dataSets/GSE12702/32.doASCRMAv2,CalMaTe,PairedPSCBS,Nsp.R inst/testScripts/complete/dataSets/GSE12702/32.doASCRMAv2,CalMaTe,PairedPSCBS,Sty.R inst/testScripts/complete/dataSets/GSE13372/01a.downloadAnnotationData.R inst/testScripts/complete/dataSets/GSE13372/01b.downloadRawData.R inst/testScripts/complete/dataSets/GSE13372/01c.installPackages.R inst/testScripts/complete/dataSets/GSE13372/21.doASCRMAv2.R inst/testScripts/complete/dataSets/GSE13372/22.doASCRMAv2,CalMaTe.R inst/testScripts/complete/dataSets/GSE13372/31.doASCRMAv2,PairedPSCBS.R inst/testScripts/complete/dataSets/GSE13372/32.doASCRMAv2,CalMaTe,PairedPSCBS.R inst/testScripts/complete/dataSets/GSE19539/01a.downloadAnnotationData.R inst/testScripts/complete/dataSets/GSE19539/01b.downloadRawData.R inst/testScripts/complete/dataSets/GSE19539/01c.installPackages.R inst/testScripts/complete/dataSets/GSE19539/21.doASCRMAv2.R inst/testScripts/complete/dataSets/GSE19539/22.doASCRMAv2,CalMaTe.R inst/testScripts/complete/dataSets/GSE20584/01a.downloadAnnotationData.R inst/testScripts/complete/dataSets/GSE20584/01b.downloadRawData.R inst/testScripts/complete/dataSets/GSE20584/01c.installPackages.R inst/testScripts/complete/dataSets/GSE20584/21.doASCRMAv2.R inst/testScripts/complete/dataSets/GSE20584/31.doASCRMAv2,PairedPSCBS.R inst/testScripts/complete/dataSets/GSE27691/01a.downloadAnnotationData.R inst/testScripts/complete/dataSets/GSE27691/01b.downloadRawData.R inst/testScripts/complete/dataSets/GSE27691/01c.installPackages.R inst/testScripts/complete/dataSets/GSE27691/21.doASCRMAv2.R inst/testScripts/complete/dataSets/GSE34754/01a.downloadAnnotationData.R inst/testScripts/complete/dataSets/GSE34754/01b.downloadRawData.R inst/testScripts/complete/dataSets/GSE34754/01c.installPackages.R inst/testScripts/complete/dataSets/GSE34754/21.doASCRMAv2.R inst/testScripts/complete/dataSets/GSE34754/22.doASCRMAv2,CalMaTe.R inst/testScripts/complete/dataSets/GSE34754/31.doASCRMAv2,PairedPSCBS.R inst/testScripts/complete/dataSets/GSE34754/32.doASCRMAv2,CalMaTe,PairedPSCBS.R inst/testScripts/futures/GenomeWideSNP_6/01a.downloadAnnotationData.R inst/testScripts/futures/GenomeWideSNP_6/01b.downloadRawData.R inst/testScripts/futures/GenomeWideSNP_6/11.AllelicCrosstalkCalibration.R inst/testScripts/futures/GenomeWideSNP_6/11.BasePositionNormalization.R inst/testScripts/futures/HG-U133_Plus_2/01a.downloadAnnotationData.R inst/testScripts/futures/HG-U133_Plus_2/01b.downloadRawData.R inst/testScripts/futures/HG-U133_Plus_2/01c.installPackages.R inst/testScripts/futures/HG-U133_Plus_2/11.OpticalBackgroundCorrection.R inst/testScripts/futures/HG-U133_Plus_2/12.GcRmaBackgroundCorrection.R inst/testScripts/futures/HG-U133_Plus_2/13.RmaBackgroundCorrection.R inst/testScripts/futures/HG-U133_Plus_2/14.NormExpBackgroundCorrection.R inst/testScripts/futures/Hs_PromPR_v02/01a.downloadAnnotationData.R inst/testScripts/futures/Hs_PromPR_v02/01b.downloadRawData.R inst/testScripts/futures/Hs_PromPR_v02/01c.installPackages.R inst/testScripts/futures/Hs_PromPR_v02/11.MatNormalization.R inst/testScripts/futures/Mapping10K_Xba142/01a.downloadAnnotationData.R inst/testScripts/futures/Mapping10K_Xba142/01b.downloadRawData.R inst/testScripts/futures/Mapping10K_Xba142/11.AllelicCrosstalkCalibration.R inst/testScripts/futures/Mapping10K_Xba142/11.BasePositionNormalization.R inst/testScripts/futures/Mapping10K_Xba142/11.UniqueCDF.R inst/testScripts/launch.R inst/testScripts/menu.R inst/testScripts/replication/chipTypes/GenomeWideSNP_6/01a.downloadAnnotationData.R inst/testScripts/replication/chipTypes/GenomeWideSNP_6/01b.downloadRawData.R inst/testScripts/replication/chipTypes/GenomeWideSNP_6/01c.installPackages.R inst/testScripts/replication/chipTypes/GenomeWideSNP_6/11.justSNPRMA_vs_oligo.R inst/testScripts/replication/chipTypes/HG-U133_Plus_2/01a.downloadAnnotationData.R inst/testScripts/replication/chipTypes/HG-U133_Plus_2/01b.downloadRawData.R inst/testScripts/replication/chipTypes/HG-U133_Plus_2/01c.installPackages.R inst/testScripts/replication/chipTypes/HG-U133_Plus_2/11.doRMA_vs_affyPLM.R inst/testScripts/replication/chipTypes/HG-U133_Plus_2/11.doRMA_vs_oligo.R inst/testScripts/replication/chipTypes/HG-U133_Plus_2/12.doGCRMA_vs_gcrma.R inst/testScripts/replication/chipTypes/HG-U133_Plus_2/21.justRMA_vs_affy.R inst/testScripts/replication/chipTypes/Hs_PromPR_v02/01a.downloadAnnotationData.R inst/testScripts/replication/chipTypes/Hs_PromPR_v02/01b.downloadRawData.R inst/testScripts/replication/chipTypes/Hs_PromPR_v02/01c.installPackages.R inst/testScripts/replication/chipTypes/Hs_PromPR_v02/11.MatNormalization_vs_MAT.R inst/testScripts/replication/chipTypes/Hs_PromPR_v02/21.MatSmoothing_vs_MAT.R inst/testScripts/replication/chipTypes/Mapping250K_Nsp/01a.downloadAnnotationData.R inst/testScripts/replication/chipTypes/Mapping250K_Nsp/01b.downloadRawData.R inst/testScripts/replication/chipTypes/Mapping250K_Nsp/01c.installPackages.R inst/testScripts/replication/chipTypes/Mapping250K_Nsp/11.justSNPRMA_vs_oligo.R inst/testScripts/replication/chipTypes/Mapping250K_Nsp/12.CRLMM_vs_oligo.R inst/testScripts/replication/chipTypes/Mapping50K_Hind240/01a.downloadAnnotData.R inst/testScripts/replication/chipTypes/Mapping50K_Hind240/01b.downloadRawData.R inst/testScripts/replication/chipTypes/Mapping50K_Hind240/01c.installPackages.R inst/testScripts/replication/chipTypes/Mapping50K_Hind240/11.justSNPRMA_vs_oligo.R inst/testScripts/replication/chipTypes/Mapping50K_Hind240/12.CRLMM_vs_oligo.R inst/testScripts/robustness/chipTypes/Mapping10K_Xba142/01a.downloadAnnotData.R inst/testScripts/robustness/chipTypes/Mapping10K_Xba142/01b.downloadRawData.R inst/testScripts/robustness/chipTypes/Mapping10K_Xba142/11.doASCRMAv1,CBS,invalid.R inst/testScripts/robustness/chipTypes/Mapping50K_Hind240/01a.downloadAnnotData.R inst/testScripts/robustness/chipTypes/Mapping50K_Hind240/01b.downloadRawData.R inst/testScripts/robustness/chipTypes/Mapping50K_Hind240/21.doASCRMAv2,CRLMM.R inst/testScripts/robustness/chipTypes/MoGene-1_0-st-v1/01a.downloadAnnotationData.R inst/testScripts/robustness/chipTypes/MoGene-1_0-st-v1/01b.downloadRawData.R inst/testScripts/robustness/chipTypes/MoGene-1_0-st-v1/11.GcRmaBgCorr.R inst/testScripts/setup.R inst/testScripts/setup/01a.downloadAllAnnotationData.R inst/testScripts/setup/01b.downloadAllRawDataSet.R inst/testScripts/setup/01c.installAllPackages.R inst/testScripts/setup/99a.cleanupRootDirectories.R inst/testScripts/system/chipTypes/CytoScanHD_Array/01a.downloadAnnotationData.R inst/testScripts/system/chipTypes/CytoScanHD_Array/01b.downloadRawData.R inst/testScripts/system/chipTypes/CytoScanHD_Array/21,doASCRMAv2,CBS.R inst/testScripts/system/chipTypes/CytoScanHD_Array/21,doASCRMAv2.R inst/testScripts/system/chipTypes/CytoScanHD_Array/21.doASCRMAv2,PSCN.R inst/testScripts/system/chipTypes/Cytogenetics_Array/01a.downloadAnnotationData.R inst/testScripts/system/chipTypes/Cytogenetics_Array/01b.downloadRawData.R inst/testScripts/system/chipTypes/Cytogenetics_Array/test20090828,cyto.R inst/testScripts/system/chipTypes/GenomeWideSNP_5/01a.downloadAnnotationData.R inst/testScripts/system/chipTypes/GenomeWideSNP_5/01b.downloadRawData.R inst/testScripts/system/chipTypes/GenomeWideSNP_5/21.doASCRMAv2,ArrayExplorer.R inst/testScripts/system/chipTypes/GenomeWideSNP_5/21.doASCRMAv2.R inst/testScripts/system/chipTypes/GenomeWideSNP_6/01a.downloadAnnotationData.R inst/testScripts/system/chipTypes/GenomeWideSNP_6/01b.downloadRawData.R inst/testScripts/system/chipTypes/GenomeWideSNP_6/01c.installPackages.R inst/testScripts/system/chipTypes/GenomeWideSNP_6/11.justSNPRMA.R inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,AlleleSummation.R inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,ArrayExplorer.R inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,GCNorm.R inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,extract.R inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,plotACC.R inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,plots.R inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,singleArray.R inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2.R inst/testScripts/system/chipTypes/HG-U133_Plus_2/01a.downloadAnnotationData.R inst/testScripts/system/chipTypes/HG-U133_Plus_2/01b.downloadRawData.R inst/testScripts/system/chipTypes/HG-U133_Plus_2/01c.installPackages.R inst/testScripts/system/chipTypes/HG-U133_Plus_2/11.doRMA,ArrayExplorer.R inst/testScripts/system/chipTypes/HG-U133_Plus_2/11.doRMA,PLM,withPriors.R inst/testScripts/system/chipTypes/HG-U133_Plus_2/11.doRMA.R inst/testScripts/system/chipTypes/HG-U133_Plus_2/12.doGCRMA.R inst/testScripts/system/chipTypes/HG-U133_Plus_2/21.BackgroundCorrections.R inst/testScripts/system/chipTypes/HG-U133_Plus_2/81.doRMA,extractAffyBatch.R inst/testScripts/system/chipTypes/HG-U133_Plus_2/81.doRMA,extractExpressionSet.R inst/testScripts/system/chipTypes/Hs_PromPR_v02/01a.downloadAnnotationData.R inst/testScripts/system/chipTypes/Hs_PromPR_v02/01b.downloadRawData.R inst/testScripts/system/chipTypes/Hs_PromPR_v02/01c.installPackages.R inst/testScripts/system/chipTypes/Hs_PromPR_v02/11.MatNormalization.R inst/testScripts/system/chipTypes/Hs_PromPR_v02/21.MatSmoothing.R inst/testScripts/system/chipTypes/Hs_PromPR_v02/31.AromaCellCpgFile.R inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/01a.downloadAnnotationData.R inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/01b.downloadRawData,GEO.R inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/01b.downloadRawData.R inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/21.doFIRMA,QC.R inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/21.doFIRMA,extras.R inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/21.doFIRMA.R inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/test20101202,gcrma.R inst/testScripts/system/chipTypes/MOUSEDIVm520650/01a.downloadAnnotationData.R inst/testScripts/system/chipTypes/MOUSEDIVm520650/01b.downloadRawData.R inst/testScripts/system/chipTypes/MOUSEDIVm520650/21.doASCRMAv2.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/01a.downloadAnnotationData.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/01b.downloadRawData.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/01c.installPackages.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/10.CDF,groupUnitsBy.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/10.CDF,readDataFrame.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/11.doCRMAv1,SmNorm.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/11.doCRMAv1.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/12.doASCRMAv1.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,CBS,any.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,CBS.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,FLN,zero.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,QA.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,extractAndWrite.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,CBS,CE.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,CBS,ref.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,GLAD.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,HaarSeg.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,PSCN.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,TotalFreqB.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,extract.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,plotACC.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,plots,pairs.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,plots.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,singleArray.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/31.ACC,BCN.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/31.ACC,mergeShifts.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/31.doASCRMAv1.ArrayExplorer.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/41.ACC,expectile.R inst/testScripts/system/chipTypes/Mapping250K_Nsp/01a.downloadAnnotationData.R inst/testScripts/system/chipTypes/Mapping250K_Nsp/01b.downloadRawData.R inst/testScripts/system/chipTypes/Mapping250K_Nsp/21.doASCRMAv1,ArrayExplorer.R inst/testScripts/system/chipTypes/Mapping250K_Nsp/31.doASCRMAv2,TumorNormalPair.R inst/testScripts/system/chipTypes/Mapping250K_Nsp/31.doASCRMAv2.R inst/testScripts/system/chipTypes/Mapping250K_Sty/01a.downloadAnnotationData.R inst/testScripts/system/chipTypes/Mapping250K_Sty/01b.downloadRawData.R inst/testScripts/system/chipTypes/Mapping250K_Sty/21.doASCRMAv2,ArrayExplorer.R inst/testScripts/system/chipTypes/Mapping250K_Sty/21.doASCRMAv2.R inst/testScripts/system/chipTypes/Mapping250K_Sty/22.doASCRMAv2,singleArray.R inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/01a.downloadAnnotData.R inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/01b.downloadRawData.R inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/11.RmaPlm.R inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/21.CRMA,QA.R inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/21.CRMA,paired.R inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/21.CRMA.R inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/31.ASCRMA.R inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/41.BCN.R inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/42.BPN,AS.R inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/42.BPN.R inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/51.ACC,merge.R inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/61.TCN,XYbias.R inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/71.doCBS,tuple.R inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/81.fnt.R inst/testScripts/system/chipTypes/Mapping50K_Hind240/01a.downloadAnnotationData.R inst/testScripts/system/chipTypes/Mapping50K_Hind240/01b.downloadRawData.R inst/testScripts/system/chipTypes/Mapping50K_Hind240/01c.installPackages.R inst/testScripts/system/chipTypes/Mapping50K_Hind240/10.CDF,groupUnitsBy.R inst/testScripts/system/chipTypes/Mapping50K_Hind240/11.justSNPRMA.R inst/testScripts/system/chipTypes/Mapping50K_Hind240/12.justSNPRMA,CRLMM.R inst/testScripts/system/chipTypes/Mapping50K_Hind240/21.doASCRMAv2,ArrayExplorer.R inst/testScripts/system/chipTypes/Mapping50K_Hind240/21.doASCRMAv2,plotACC.R inst/testScripts/system/chipTypes/Mapping50K_Hind240/21.doASCRMAv2.R inst/testScripts/system/chipTypes/Mm_PromPR_v02/01a.downloadAnnotationData.R inst/testScripts/system/chipTypes/Mm_PromPR_v02/10,CDF,unique.R inst/testScripts/system/chipTypes/MoEx-1_0-st-v1/01a.downloadAnnotationData.R inst/testScripts/system/chipTypes/MoEx-1_0-st-v1/01b.downloadRawData.R inst/testScripts/system/chipTypes/MoEx-1_0-st-v1/11.GcRmaBackgroundCorrection.R inst/testScripts/system/chipTypes/MoGene-1_0-st-v1/01a.downloadAnnotationData.R inst/testScripts/system/chipTypes/MoGene-1_0-st-v1/01b.downloadRawData.R inst/testScripts/system/chipTypes/MoGene-1_0-st-v1/11.RmaBackgroundCorrection.R inst/testScripts/system/chipTypes/MoGene-1_0-st-v1/12.QuantileNormalization.R inst/testScripts/system/chipTypes/Test3/01a.downloadAnnotationData.R inst/testScripts/system/chipTypes/Test3/01c.installPackages.R inst/testScripts/system/chipTypes/Test3/01d.downloadRawData.R inst/testScripts/system/chipTypes/Test3/11.ArrayExplorer.R inst/testScripts/testAll.R inst/vignettes/CRMA,Mapping50K_Hind240,BiasCorrectedChrXY.R inst/vignettes/CRMAv2,Mapping50K_Hind240.R inst/vignettes/replication-CRLMM/R/01a.downloadAnnotData.R inst/vignettes/replication-CRLMM/R/01b.downloadRawData.R inst/vignettes/replication-GCRMA/R/01a.downloadAnnotData.R inst/vignettes/replication-GCRMA/R/01b.downloadRawData.R inst/vignettes/replication-MAT/R/01a.downloadAnnotationData.R inst/vignettes/replication-MAT/R/01b.downloadRawData.R 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tests/002.setupExampleData,rawData.R tests/AffymetrixCdfFile.R tests/AffymetrixCelFile.R tests/AffymetrixCelSet.R