Files in HenrikBengtsson/aroma

An R Object-oriented Microarray Analysis package

R/000.R R/006.fixVarArgs.R R/999.NonDocumentedObjects.R R/999.package.R R/9999.DEPRECATED.BFilter.R R/9999.DEPRECATED.BMAData.R R/9999.DEPRECATED.File.ARGS.R R/9999.DEPRECATED.Layout.R R/9999.DEPRECATED.MAData.R R/9999.DEPRECATED.MicroarrayData.R R/9999.DEPRECATED.RGData.R R/9999.DEPRECATED.RawData.R R/9999.DEPRECATED.Replicates.R R/9999.DEPRECATED.TFilter.R R/9999.DEPRECATED.TMAData.R R/AFilter.R R/AcceptFilter.R R/AffineModelFit.R R/Analyzer.R R/AndFilter.R R/Array.R R/DfFilter.R R/ExperimentalSetup.R R/ExpressionData.R R/FieldFilter.R R/Filter.R R/GSRArray.R R/GalLayout.R R/GeneAcceptFilter.R R/GeneGroups.R R/GenePixData.R R/GeneRejectFilter.R R/GeneReplicateSlideArray.R R/GeneSlideArray.R R/ImaGeneData.R R/Layout.R R/LayoutGroups.R R/MAData.NORM.R R/MAData.R R/MFilter.R R/Matrix.R R/MicroarrayArray.R R/MicroarrayData.ARGS.R R/MicroarrayData.IO.R R/MicroarrayData.NORM.R R/MicroarrayData.PLOT.R R/MicroarrayData.R R/MicroarrayData.WEIGHTS.R R/MultiwayArray.R R/NotFilter.R R/OnWeights.R R/OrFilter.R R/ParallelFilter.R R/PrintdipGroups.R R/PrinttipGroups.R R/QuantArrayData.R R/RGData.NORM.R R/RGData.R R/RGData.fitIWPCA.R R/RawData.NORM.R R/RawData.R R/RejectFilter.R R/SEFilter.R R/SMA.R R/SSMatrix.R R/ScanAlyze20Data.R R/ScanAlyzeData.R R/SerialFilter.R R/SpotData.R R/SpotPosition.R R/SpotSlideArray.R R/SpotfinderData.R R/Weights.R R/log.na.R R/private.utils.R R/zzz.R man/AFilter.Rd man/AcceptFilter.Rd man/AffineModelFit.Rd man/AndFilter.Rd man/DfFilter.Rd man/ExperimentalSetup.Rd man/FieldFilter.Rd man/Filter.Rd man/GalLayout.Rd man/GeneAcceptFilter.Rd man/GeneGroups.Rd man/GenePixData.Rd man/GeneRejectFilter.Rd man/ImaGeneData.Rd man/Layout.Rd man/LayoutGroups.Rd man/MAData.Rd man/MFilter.Rd man/MicroarrayData.Rd man/Non-documented_objects.Rd man/NotFilter.Rd man/OrFilter.Rd man/ParallelFilter.Rd man/PlateGroups.Rd man/PrintdipGroups.Rd man/PrinttipGroups.Rd man/QuantArrayData.Rd man/RGData.Rd man/RawData.Rd man/RejectFilter.Rd man/SEFilter.Rd man/SMA.Rd man/ScanAlyze20Data.Rd man/ScanAlyzeData.Rd man/SerialFilter.Rd man/SlideColumnGroups.Rd man/SlideRowGroups.Rd man/SpotData.Rd man/SpotPosition.Rd man/SpotfinderData.Rd man/Weights.Rd man/addFlag.MicroarrayData.Rd man/append.MicroarrayData.Rd man/aroma-package.Rd man/as.MAData.RGData.Rd man/as.RG.SMA.Rd man/as.RGData.MAData.Rd man/as.character.SpotPosition.Rd man/as.data.frame.MicroarrayData.Rd man/as.data.frame.SpotPosition.Rd man/as.layout.SMA.Rd man/boxplot.MicroarrayData.Rd man/calibrateMultiscan.RGData.Rd man/changeInput.Filter.Rd man/changeInput.ParallelFilter.Rd man/changeInput.SerialFilter.Rd man/clearFlag.MicroarrayData.Rd man/convertFieldNames.GenePixData.Rd man/equals.Layout.Rd man/equals.MicroarrayData.Rd man/estimateMACurve.MAData.Rd man/extract.MicroarrayData.Rd man/findSetupFiles.ExperimentalSetup.Rd man/fitMultiscanAffine.RGData.Rd man/fromSaturatedSignals.SignalWeights.Rd man/getAdjustedSpotVariability.MAData.Rd man/getArea.GenePixData.Rd man/getAspectRatio.SpotPosition.Rd man/getBackground.RawData.Rd man/getBackgroundSD.GenePixData.Rd man/getBottomEdge.SpotPosition.Rd man/getChannelNames.GenePixData.Rd man/getChannelNames.MicroarrayData.Rd man/getColors.MAData.Rd man/getColors.RGData.Rd man/getColors.RawData.Rd man/getDistancesTo.SpotPosition.Rd man/getDuplicates.GeneGroups.Rd man/getExtra.MicroarrayData.Rd man/getFieldNames.MicroarrayData.Rd man/getFlag.MicroarrayData.Rd man/getForeground.RawData.Rd man/getForegroundSD.GenePixData.Rd man/getForegroundSD.SpotData.Rd man/getForegroundSE.GenePixData.Rd man/getForegroundSE.SpotData.Rd man/getGeneSlideReplicateIndex.MicroarrayData.Rd man/getGeneVariability.MAData.Rd man/getId.Layout.Rd man/getIndex.AcceptFilter.Rd man/getIndex.AndFilter.Rd man/getIndex.FieldFilter.Rd man/getIndex.Filter.Rd man/getIndex.Layout.Rd man/getIndex.OrFilter.Rd man/getIndices.Layout.Rd man/getInput.Filter.Rd man/getInput.ParallelFilter.Rd man/getInput.SerialFilter.Rd man/getLabel.MicroarrayData.Rd man/getLayout.MicroarrayData.Rd man/getLeftEdge.SpotPosition.Rd man/getLocation.Layout.Rd man/getLogIntensities.RGData.Rd man/getLogRatios.RGData.Rd man/getMOR.MAData.Rd man/getMOR2003a.MAData.Rd man/getMaxHeight.SpotPosition.Rd man/getMaxWidth.SpotPosition.Rd man/getName.Layout.Rd man/getNames.GeneGroups.Rd man/getParameter.Filter.Rd man/getPosition.Layout.Rd man/getPrintorder.Layout.Rd man/getQuadruplicates.GeneGroups.Rd man/getRawData.GenePixData.Rd man/getRawData.ImaGeneData.Rd man/getRawData.QuantArrayData.Rd man/getRawData.ScanAlyzeData.Rd man/getRawData.SpotData.Rd man/getRawData.SpotfinderData.Rd man/getReplicates.GeneGroups.Rd man/getRightEdge.SpotPosition.Rd man/getSignal.RawData.Rd man/getSizes.GeneGroups.Rd man/getSlideNames.MicroarrayData.Rd man/getSpotPosition.GenePixData.Rd man/getSpotPosition.ImaGeneData.Rd man/getSpotPosition.QuantArrayData.Rd man/getSpotPosition.ScanAlyze20Data.Rd man/getSpotPosition.ScanAlyzeData.Rd man/getSpotPosition.SpotData.Rd man/getSpots.GeneGroups.Rd man/getTopEdge.SpotPosition.Rd man/getTriplicates.GeneGroups.Rd man/getVisible.Filter.Rd man/gridSize.Layout.Rd man/hasLayout.MicroarrayData.Rd man/highlight.Filter.Rd man/highlight.MicroarrayData.Rd man/hist.MicroarrayData.Rd man/indexOf.Layout.Rd man/isSaturated.MicroarrayData.Rd man/keepSlides.MicroarrayData.Rd man/keepSpots.MicroarrayData.Rd man/listFlags.MicroarrayData.Rd man/loessQuantile.MAData.Rd man/lowessCurve.MicroarrayData.Rd man/mean.MAData.Rd man/mean.RGData.Rd man/nbrOfColumns.Layout.Rd man/nbrOfFields.MicroarrayData.Rd man/nbrOfGrids.Layout.Rd man/nbrOfGroups.GeneGroups.Rd man/nbrOfRows.Layout.Rd man/nbrOfSlides.MicroarrayData.Rd man/nbrOfSlides.SpotPosition.Rd man/nbrOfSpots.Layout.Rd man/nbrOfSpots.MicroarrayData.Rd man/nbrOfSpots.SpotPosition.Rd man/normalizeAcrossSlides.MAData.Rd man/normalizeAffine.MAData.Rd man/normalizeAffine.RGData.Rd man/normalizeAffineShift.MAData.Rd man/normalizeCurveFit.MAData.Rd man/normalizeCurveFit.RGData.Rd man/normalizeLogRatioShift.MAData.Rd man/normalizePlatewise.MicroarrayData.Rd man/normalizeWithinSlide.MAData.Rd man/plot.MicroarrayData.Rd man/plot.SpotPosition.Rd man/plotDensity.MicroarrayData.Rd man/plotMvsM.MAData.Rd man/plotPrintorder.MicroarrayData.Rd man/plotSpatial.GenePixData.Rd man/plotSpatial.MicroarrayData.Rd man/plotSpatial.QuantArrayData.Rd man/plotSpatial.ScanAlyzeData.Rd man/plotSpatial.SpotData.Rd man/plotSpatial.SpotfinderData.Rd man/plotSpatial3d.MicroarrayData.Rd man/plotXY.MicroarrayData.Rd man/points.SpotPosition.Rd man/read.ExperimentalSetup.Rd man/read.GalLayout.Rd man/read.GenePixData.Rd man/read.ImaGeneData.Rd man/read.Layout.Rd man/read.MicroarrayData.Rd man/read.QuantArrayData.Rd man/read.ScanAlyze20Data.Rd man/read.ScanAlyzeData.Rd man/read.SpotData.Rd man/read.SpotfinderData.Rd man/readHeader.GenePixData.Rd man/readOneFile.QuantArrayData.Rd man/readOneFile.SpotfinderData.Rd man/removeSlides.MicroarrayData.Rd man/removeSpots.MicroarrayData.Rd man/select.MicroarrayData.Rd man/set.Layout.Rd man/setExtra.MicroarrayData.Rd man/setFlag.MicroarrayData.Rd man/setId.Layout.Rd man/setLabel.MicroarrayData.Rd man/setLayout.MicroarrayData.Rd man/setName.Layout.Rd man/setParameter.Filter.Rd man/setProbeWeights.MicroarrayData.Rd man/setSaturated.MicroarrayData.Rd man/setSlideNames.MicroarrayData.Rd man/setVisible.Filter.Rd man/shift.MAData.Rd man/shift.RGData.Rd man/shift.RawData.Rd man/size.Layout.Rd man/size.MicroarrayData.Rd man/size.SpotPosition.Rd man/str.MicroarrayData.Rd man/subplots.MicroarrayData.Rd man/summary.MicroarrayData.Rd man/swapDyes.MAData.Rd man/swapDyes.RGData.Rd man/swapDyes.RawData.Rd man/text.Filter.Rd man/text.MicroarrayData.Rd man/toPrintorderMatrix.Layout.Rd man/toXYMatrix.Layout.Rd man/topSpots.MAData.Rd man/unite.MicroarrayWeights.Rd man/validateArgumentChannels.GenePixData.Rd man/validateArgumentGroupBy.MicroarrayData.Rd man/validateArgumentSlide.MicroarrayData.Rd man/validateArgumentSlides.MicroarrayData.Rd man/validateArgumentWeights.MicroarrayData.Rd man/var.MAData.Rd man/var.RGData.Rd man/write.GenePixData.Rd man/write.ImaGeneData.Rd man/write.Layout.Rd man/write.MicroarrayData.Rd man/write.QuantArrayData.Rd man/write.ScanAlyze20Data.Rd man/write.ScanAlyzeData.Rd man/write.SpotData.Rd man/write.SpotPosition.Rd man/write.SpotfinderData.Rd