API for HenrikBengtsson/aroma
An R Object-oriented Microarray Analysis package

Global functions
AFilter	Man page
AcceptFilter	Man page
AcceptFilter.getIndex	Man page
AffineModelFit	Man page
Analyzer	Man page
AndFilter	Man page
AndFilter.getIndex	Man page
Array	Man page
BFilter	Man page
BMAData	Man page
DesignMatrix	Man page
DfFilter	Man page
ExperimentalSetup	Man page
ExperimentalSetup.findSetupFiles	Man page
ExperimentalSetup.read	Man page
ExpressionData	Man page
FieldFilter	Man page
FieldFilter.getIndex	Man page
Filter	Man page
Filter.changeInput	Man page
Filter.getIndex	Man page
Filter.getInput	Man page
Filter.getParameter	Man page
Filter.getVisible	Man page
Filter.highlight	Man page
Filter.setParameter	Man page
Filter.setVisible	Man page
Filter.text	Man page
GSRArray	Man page
GalLayout	Man page
GalLayout.read	Man page
GeneAcceptFilter	Man page
GeneGroups	Man page
GeneGroups.getDuplicates	Man page
GeneGroups.getNames	Man page
GeneGroups.getQuadruplicates	Man page
GeneGroups.getReplicates	Man page
GeneGroups.getSizes	Man page
GeneGroups.getSpots	Man page
GeneGroups.getTriplicates	Man page
GeneGroups.nbrOfGroups	Man page
GenePixData	Man page
GenePixData.convertFieldNames	Man page
GenePixData.getArea	Man page
GenePixData.getBackgroundSD	Man page
GenePixData.getChannelNames	Man page
GenePixData.getForegroundSD	Man page
GenePixData.getForegroundSE	Man page
GenePixData.getRawData	Man page
GenePixData.getSpotPosition	Man page
GenePixData.plotSpatial	Man page
GenePixData.read	Man page
GenePixData.readHeader	Man page
GenePixData.validateArgumentChannels	Man page
GenePixData.write	Man page
GeneRejectFilter	Man page
GeneReplicateSlideArray	Man page
GeneSlideArray	Man page
ImaGeneData	Man page
ImaGeneData.getRawData	Man page
ImaGeneData.getSpotPosition	Man page
ImaGeneData.read	Man page
ImaGeneData.write	Man page
Layout	Man page
Layout.equals	Man page
Layout.getId	Man page
Layout.getIndex	Man page
Layout.getIndices	Man page
Layout.getLocation	Man page
Layout.getName	Man page
Layout.getPosition	Man page
Layout.getPrintorder	Man page
Layout.gridSize	Man page
Layout.indexOf	Man page
Layout.nbrOfColumns	Man page
Layout.nbrOfGrids	Man page
Layout.nbrOfRows	Man page
Layout.nbrOfSpots	Man page
Layout.read	Man page
Layout.set	Man page
Layout.setId	Man page
Layout.setName	Man page
Layout.size	Man page
Layout.toPrintorderMatrix	Man page
Layout.toXYMatrix	Man page
Layout.write	Man page
LayoutGroups	Man page
MAData	Man page
MAData.as.RGData	Man page
MAData.estimateMACurve	Man page
MAData.getAdjustedSpotVariability	Man page
MAData.getColors	Man page
MAData.getGeneVariability	Man page
MAData.getMOR	Man page
MAData.getMOR2003a	Man page
MAData.loessQuantile	Man page
MAData.mean	Man page
MAData.normalizeAcrossSlides	Man page
MAData.normalizeAffine	Man page
MAData.normalizeAffineShift	Man page
MAData.normalizeCurveFit	Man page
MAData.normalizeLogRatioShift	Man page
MAData.normalizeWithinSlide	Man page
MAData.plotMvsM	Man page
MAData.shift	Man page
MAData.swapDyes	Man page
MAData.topSpots	Man page
MAData.var	Man page
MFilter	Man page
Matrix	Man page
MicroarrayArray	Man page
MicroarrayData	Man page
MicroarrayData.addFlag	Man page
MicroarrayData.append	Man page
MicroarrayData.as.data.frame	Man page
MicroarrayData.boxplot	Man page
MicroarrayData.clearFlag	Man page
MicroarrayData.equals	Man page
MicroarrayData.extract	Man page
MicroarrayData.getChannelNames	Man page
MicroarrayData.getExtra	Man page
MicroarrayData.getFieldNames	Man page
MicroarrayData.getFlag	Man page
MicroarrayData.getGeneSlideReplicateIndex	Man page
MicroarrayData.getLabel	Man page
MicroarrayData.getLayout	Man page
MicroarrayData.getSlideNames	Man page
MicroarrayData.hasLayout	Man page
MicroarrayData.highlight	Man page
MicroarrayData.hist	Man page
MicroarrayData.isSaturated	Man page
MicroarrayData.keepSlides	Man page
MicroarrayData.keepSpots	Man page
MicroarrayData.listFlags	Man page
MicroarrayData.lowessCurve	Man page
MicroarrayData.nbrOfFields	Man page
MicroarrayData.nbrOfSlides	Man page
MicroarrayData.nbrOfSpots	Man page
MicroarrayData.normalizePlatewise	Man page
MicroarrayData.plot	Man page
MicroarrayData.plotDensity	Man page
MicroarrayData.plotPrintorder	Man page
MicroarrayData.plotSpatial	Man page
MicroarrayData.plotSpatial3d	Man page
MicroarrayData.plotXY	Man page
MicroarrayData.read	Man page
MicroarrayData.removeSlides	Man page
MicroarrayData.removeSpots	Man page
MicroarrayData.select	Man page
MicroarrayData.setExtra	Man page
MicroarrayData.setFlag	Man page
MicroarrayData.setLabel	Man page
MicroarrayData.setLayout	Man page
MicroarrayData.setProbeWeights	Man page
MicroarrayData.setSaturated	Man page
MicroarrayData.setSlideNames	Man page
MicroarrayData.size	Man page
MicroarrayData.str	Man page
MicroarrayData.subplots	Man page
MicroarrayData.summary	Man page
MicroarrayData.text	Man page
MicroarrayData.validateArgumentGroupBy	Man page
MicroarrayData.validateArgumentSlide	Man page
MicroarrayData.validateArgumentSlides	Man page
MicroarrayData.validateArgumentWeights	Man page
MicroarrayData.write	Man page
MicroarrayWeights	Man page
MicroarrayWeights.unite	Man page
MultiwayArray	Man page
Non-documented objects	Man page
NotFilter	Man page
OrFilter	Man page
OrFilter.getIndex	Man page
ParallelFilter	Man page
ParallelFilter.changeInput	Man page
ParallelFilter.getInput	Man page
PlateGroups	Man page
PrintdipGroups	Man page
PrinttipGroups	Man page
ProbeWeights	Man page
QuantArrayData	Man page
QuantArrayData.getRawData	Man page
QuantArrayData.getSpotPosition	Man page
QuantArrayData.plotSpatial	Man page
QuantArrayData.read	Man page
QuantArrayData.readOneFile	Man page
QuantArrayData.write	Man page
RGData	Man page
RGData.as.MAData	Man page
RGData.calibrateMultiscan	Man page
RGData.fitMultiscanAffine	Man page
RGData.getColors	Man page
RGData.getLogIntensities	Man page
RGData.getLogRatios	Man page
RGData.mean	Man page
RGData.normalizeAffine	Man page
RGData.normalizeCurveFit	Man page
RGData.shift	Man page
RGData.swapDyes	Man page
RGData.var	Man page
RawData	Man page
RawData.getBackground	Man page
RawData.getColors	Man page
RawData.getForeground	Man page
RawData.getSignal	Man page
RawData.shift	Man page
RawData.swapDyes	Man page
RejectFilter	Man page
Replicates	Man page
SEFilter	Man page
SMA	Man page
SMA.as.RG	Man page
SMA.as.layout	Man page
SSMatrix	Man page
ScanAlyze20Data	Man page
ScanAlyze20Data.getSpotPosition	Man page
ScanAlyze20Data.read	Man page
ScanAlyze20Data.write	Man page
ScanAlyzeData	Man page
ScanAlyzeData.getRawData	Man page
ScanAlyzeData.getSpotPosition	Man page
ScanAlyzeData.plotSpatial	Man page
ScanAlyzeData.read	Man page
ScanAlyzeData.write	Man page
SerialFilter	Man page
SerialFilter.changeInput	Man page
SerialFilter.getInput	Man page
SignalWeights	Man page
SignalWeights.fromSaturatedSignals	Man page
SlideColumnGroups	Man page
SlideRowGroups	Man page
SpotData	Man page
SpotData.getForegroundSD	Man page
SpotData.getForegroundSE	Man page
SpotData.getRawData	Man page
SpotData.getSpotPosition	Man page
SpotData.plotSpatial	Man page
SpotData.read	Man page
SpotData.write	Man page
SpotPosition	Man page
SpotPosition.as.character	Man page
SpotPosition.as.data.frame	Man page
SpotPosition.getAspectRatio	Man page
SpotPosition.getBottomEdge	Man page
SpotPosition.getDistancesTo	Man page
SpotPosition.getLeftEdge	Man page
SpotPosition.getMaxHeight	Man page
SpotPosition.getMaxWidth	Man page
SpotPosition.getRightEdge	Man page
SpotPosition.getTopEdge	Man page
SpotPosition.nbrOfSlides	Man page
SpotPosition.nbrOfSpots	Man page
SpotPosition.plot	Man page
SpotPosition.points	Man page
SpotPosition.size	Man page
SpotPosition.write	Man page
SpotSlideArray	Man page
SpotfinderData	Man page
SpotfinderData.getRawData	Man page
SpotfinderData.plotSpatial	Man page
SpotfinderData.read	Man page
SpotfinderData.readOneFile	Man page
SpotfinderData.write	Man page
SuperGroups	Man page
TFilter	Man page
TMAData	Man page
Weights	Man page
[.MicroarrayArray	Man page
[<-.MicroarrayArray	Man page
addFlag	Man page
addFlag,MicroarrayData-method	Man page
addFlag.MicroarrayData	Man page Man page
anonymize	Man page
anonymize.GenePixData	Man page
anonymize.ImaGeneData	Man page
anonymize.Layout	Man page
anonymize.QuantArrayData	Man page
append	Man page
append,MicroarrayData-method	Man page
append.GenePixData	Man page
append.MicroarrayData	Man page Man page
append.ScanAlyzeData	Man page
append.SpotData	Man page
append.SpotfinderData	Man page
append.default	Man page
apply	Man page
apply.GSRArray	Man page
apply.LayoutGroups	Man page
apply.MultiwayArray	Man page
apply.default	Man page
applyGenewise	Man page
applyGenewise.MicroarrayData	Man page
applyGroupwise	Man page
applyGroupwise.MicroarrayData	Man page
applyPlatewise	Man page
applyPlatewise.MicroarrayData	Man page
applyPrintdipwise	Man page
applyPrintdipwise.MicroarrayData	Man page
applyPrinttipwise	Man page
applyPrinttipwise.MicroarrayData	Man page
aroma	Man page
aroma-package	Man page
as.BMAData	Man page
as.BMAData.BMAData	Man page
as.BMAData.MAData	Man page
as.BMAData.default	Man page
as.DataFrame	Man page
as.DataFrame.Matrix	Man page
as.GeneReplicateSlideArray	Man page
as.GeneReplicateSlideArray.MicroarrayArray	Man page
as.GeneSlideArray	Man page
as.GeneSlideArray.MicroarrayArray	Man page
as.Layout	Man page
as.Layout.Layout	Man page
as.Layout.default	Man page
as.MAData	Man page
as.MAData,RGData-method	Man page
as.MAData.MAData	Man page
as.MAData.RGData	Man page Man page
as.MAData.default	Man page
as.RG	Man page
as.RG,SMA-method	Man page
as.RG.SMA	Man page Man page
as.RGData	Man page
as.RGData,MAData-method	Man page
as.RGData.MAData	Man page Man page
as.RGData.RGData	Man page
as.RGData.RawData	Man page
as.RGData.default	Man page
as.RawData	Man page
as.RawData.GenePixData	Man page
as.RawData.ImaGeneData	Man page
as.RawData.MAData	Man page
as.RawData.QuantArrayData	Man page
as.RawData.RGData	Man page
as.RawData.RawData	Man page
as.RawData.ScanAlyzeData	Man page
as.RawData.SpotData	Man page
as.RawData.SpotfinderData	Man page
as.RawData.default	Man page
as.SpotSlideArray	Man page
as.SpotSlideArray.MicroarrayArray	Man page
as.TMAData	Man page
as.TMAData.MAData	Man page
as.TMAData.TMAData	Man page
as.TMAData.default	Man page
as.character,SpotPosition-method	Man page
as.character.AffineModelFit	Man page
as.character.BMAData	Man page
as.character.ExperimentalSetup	Man page
as.character.Filter	Man page
as.character.GSRArray	Man page
as.character.GeneAcceptFilter	Man page
as.character.GeneGroups	Man page
as.character.GeneRejectFilter	Man page
as.character.Layout	Man page
as.character.LayoutGroups	Man page
as.character.MAData	Man page
as.character.MicroarrayData	Man page
as.character.PlateGroups	Man page
as.character.PrintdipGroups	Man page
as.character.PrinttipGroups	Man page
as.character.RGData	Man page
as.character.RawData	Man page
as.character.Replicates	Man page
as.character.SlideColumnGroups	Man page
as.character.SlideRowGroups	Man page
as.character.SpotPosition	Man page Man page
as.character.SuperGroups	Man page
as.character.TMAData	Man page
as.data.frame	Man page
as.data.frame,MicroarrayData-method	Man page
as.data.frame,SpotPosition-method	Man page
as.data.frame.Array	Man page
as.data.frame.ExperimentalSetup	Man page
as.data.frame.GalLayout	Man page
as.data.frame.Layout	Man page
as.data.frame.MicroarrayData	Man page Man page
as.data.frame.SpotPosition	Man page Man page
as.layout	Man page
as.layout,SMA-method	Man page
as.layout.SMA	Man page Man page
as.matrix	Man page
as.matrix.DesignMatrix	Man page
as.matrix.GeneSlideArray	Man page
as.matrix.MicroarrayArray	Man page
as.matrix.SpotSlideArray	Man page
asGSRArray	Man page
asGSRArray.GSRArray	Man page
asGSRArray.SSMatrix	Man page
asGSRArray.default	Man page
asGSRArray.matrix	Man page
asSSMatrix	Man page
asSSMatrix.GSRArray	Man page
asSSMatrix.SSMatrix	Man page
asSSMatrix.default	Man page
asSSMatrix.matrix	Man page
backtransformAffine	Man page
boxplot,MicroarrayData-method	Man page
boxplot.MAData	Man page
boxplot.MicroarrayData	Man page Man page
boxplot.RGData	Man page
boxplot.RawData	Man page
calibrateMultiscan	Man page
calibrateMultiscan,RGData-method	Man page
calibrateMultiscan.RGData	Man page Man page
calibrateMultiscan.RawData	Man page
changeInput	Man page
changeInput,Filter-method	Man page
changeInput,ParallelFilter-method	Man page
changeInput,SerialFilter-method	Man page
changeInput.Filter	Man page Man page
changeInput.ParallelFilter	Man page Man page
changeInput.SerialFilter	Man page Man page
clearCache	Man page
clearCache.MicroarrayData	Man page
clearFlag	Man page
clearFlag,MicroarrayData-method	Man page
clearFlag.MicroarrayData	Man page Man page
coef.AffineModelFit	Man page
com.braju.sma.dimStr	Man page
convertFieldNames	Man page
convertFieldNames,GenePixData-method	Man page
convertFieldNames.GenePixData	Man page Man page
createColors	Man page
createColors.MicroarrayData	Man page
dataFrameToList	Man page
dataFrameToList.MicroarrayData	Man page
diff.MultiwayArray	Man page
dim<-.GSRArray	Man page
drawCurveFit	Man page
drawCurveFit.MAData	Man page
equals,Layout-method	Man page
equals,MicroarrayData-method	Man page
equals.Layout	Man page Man page
equals.MicroarrayData	Man page Man page
equals.Replicates	Man page
equals.SpotPosition	Man page
estimateMACurve	Man page
estimateMACurve,MAData-method	Man page
estimateMACurve.MAData	Man page Man page
extract	Man page
extract,MicroarrayData-method	Man page
extract.MicroarrayData	Man page Man page
extract.SpotPosition	Man page
extractLayout	Man page
extractLayout.SpotData	Man page
extractLayout.SpotfinderData	Man page
findChannelBiasDifferences	Man page
findChannelBiasDifferences.RGData	Man page
findSetupFiles	Man page
findSetupFiles,ExperimentalSetup-method	Man page
findSetupFiles.ExperimentalSetup	Man page Man page
fitIWPCA	Man page
fitIWPCA.RGData	Man page
fitMultiscanAffine	Man page
fitMultiscanAffine,RGData-method	Man page
fitMultiscanAffine.RGData	Man page Man page
fitted.AffineModelFit	Man page
flip.Matrix	Man page
fromDataFrame	Man page
fromDataFrame.Layout	Man page
fromLayout	Man page
fromLayout.Replicates	Man page
fromSSMatrix	Man page
fromSSMatrix.GSRArray	Man page
fromSaturatedSignals	Man page
fromSaturatedSignals,SignalWeights-method	Man page
fromSaturatedSignals.SignalWeights	Man page Man page
fromType	Man page
fromType.Replicates	Man page
getA	Man page
getA.AffineModelFit	Man page
getA.RGData	Man page
getADiagonal	Man page
getADiagonal.AffineModelFit	Man page
getAbscent	Man page
getAbscent.GenePixData	Man page
getAbscent.ImaGeneData	Man page
getAbsolutePath.MicroarrayData	Man page
getAdjustedSpotVariability	Man page
getAdjustedSpotVariability,MAData-method	Man page
getAdjustedSpotVariability.MAData	Man page Man page
getArea	Man page
getArea,GenePixData-method	Man page
getArea.GenePixData	Man page Man page
getArea.ImaGeneData	Man page
getArea.QuantArrayData	Man page
getArea.ScanAlyze20Data	Man page
getArea.ScanAlyzeData	Man page
getArea.SpotData	Man page
getArea.SpotfinderData	Man page
getArrayAspectRatio	Man page
getArrayAspectRatio.GenePixData	Man page
getArrayAspectRatio.SpotData	Man page
getArrayBottom	Man page
getArrayBottom.GenePixData	Man page
getArrayBottom.SpotData	Man page
getArrayHeight	Man page
getArrayHeight.GenePixData	Man page
getArrayHeight.SpotData	Man page
getArrayLeft	Man page
getArrayLeft.GenePixData	Man page
getArrayLeft.SpotData	Man page
getArrayRight	Man page
getArrayRight.GenePixData	Man page
getArrayRight.SpotData	Man page
getArrayTop	Man page
getArrayTop.GenePixData	Man page
getArrayTop.SpotData	Man page
getArrayWidth	Man page
getArrayWidth.GenePixData	Man page
getArrayWidth.SpotData	Man page
getAspectRatio,SpotPosition-method	Man page
getAspectRatio.SpotPosition	Man page Man page
getB	Man page
getB.AffineModelFit	Man page
getBackground	Man page
getBackground,RawData-method	Man page
getBackground.GenePixData	Man page
getBackground.QuantArrayData	Man page
getBackground.RawData	Man page Man page
getBackground.ScanAlyze20Data	Man page
getBackground.ScanAlyzeData	Man page
getBackground.SpotData	Man page
getBackground.SpotfinderData	Man page
getBackgroundArea	Man page
getBackgroundArea.GenePixData	Man page
getBackgroundSD	Man page
getBackgroundSD,GenePixData-method	Man page
getBackgroundSD.GenePixData	Man page Man page
getBackgroundSD.QuantArrayData	Man page
getBackgroundSD.ScanAlyze20Data	Man page
getBad	Man page
getBad.GenePixData	Man page
getBgArea	Man page
getBgArea.GenePixData	Man page
getBgArea.ImaGeneData	Man page
getBgArea.ScanAlyze20Data	Man page
getBgArea.ScanAlyzeData	Man page
getBgArea.SpotData	Man page
getBgArea.SpotfinderData	Man page
getBlank	Man page
getBlank.Layout	Man page
getBlank.MicroarrayData	Man page
getBlock	Man page
getBlock.GalLayout	Man page
getBottomEdge	Man page
getBottomEdge,SpotPosition-method	Man page
getBottomEdge.SpotPosition	Man page Man page
getCache	Man page
getCache.MicroarrayData	Man page
getCalibratedMultiscan	Man page
getCalibratedMultiscan.RGData	Man page
getChannelNames	Man page
getChannelNames,GenePixData-method	Man page
getChannelNames,MicroarrayData-method	Man page
getChannelNames.GenePixData	Man page Man page
getChannelNames.MicroarrayData	Man page Man page
getChannelNames.RGData	Man page
getCircularity	Man page
getCircularity.GenePixData	Man page
getCircularity.ImaGeneData	Man page
getCircularity.ScanAlyzeData	Man page
getCircularity.SpotData	Man page
getCircularity.SpotfinderData	Man page
getCoefficients	Man page
getCoefficients.AffineModelFit	Man page
getColors,MAData-method	Man page
getColors,RGData-method	Man page
getColors,RawData-method	Man page
getColors.MAData	Man page Man page
getColors.MicroarrayData	Man page
getColors.RGData	Man page Man page
getColors.RawData	Man page Man page
getColors.TMAData	Man page
getColumn	Man page
getColumn.GalLayout	Man page
getDataFiles	Man page
getDataFiles.ExperimentalSetup	Man page
getDegreesOfFreedom	Man page
getDegreesOfFreedom.TMAData	Man page
getDenseSpots	Man page
getDenseSpots.MAData	Man page
getDesignMatrix	Man page
getDesignMatrix.Analyzer	Man page
getDiameter	Man page
getDiameter.ScanAlyze20Data	Man page
getDiameter.ScanAlyzeData	Man page
getDistance	Man page
getDistance.AffineModelFit	Man page
getDistancesTo	Man page
getDistancesTo,SpotPosition-method	Man page
getDistancesTo.SpotPosition	Man page Man page
getDuplicates	Man page
getDuplicates,GeneGroups-method	Man page
getDuplicates.GeneGroups	Man page Man page
getDyesUsed	Man page
getDyesUsed.ExperimentalSetup	Man page
getExcludedSpots	Man page
getExcludedSpots.MicroarrayData	Man page
getExtra	Man page
getExtra,MicroarrayData-method	Man page
getExtra.MicroarrayData	Man page Man page
getExtreme	Man page
getExtreme.MicroarrayData	Man page
getField	Man page
getField.MicroarrayData	Man page
getFieldNames	Man page
getFieldNames,MicroarrayData-method	Man page
getFieldNames.GalLayout	Man page
getFieldNames.MicroarrayData	Man page Man page
getFirst	Man page
getFirst.PlateGroups	Man page
getFlag	Man page
getFlag,MicroarrayData-method	Man page
getFlag.MicroarrayData	Man page Man page
getFocusPosition	Man page
getFocusPosition.GenePixData	Man page
getForeground	Man page
getForeground,RawData-method	Man page
getForeground.GenePixData	Man page
getForeground.QuantArrayData	Man page
getForeground.RawData	Man page Man page
getForeground.ScanAlyze20Data	Man page
getForeground.ScanAlyzeData	Man page
getForeground.SpotData	Man page
getForeground.SpotfinderData	Man page
getForegroundSD	Man page
getForegroundSD,GenePixData-method	Man page
getForegroundSD,SpotData-method	Man page
getForegroundSD.GenePixData	Man page Man page
getForegroundSD.QuantArrayData	Man page
getForegroundSD.ScanAlyze20Data	Man page
getForegroundSD.SpotData	Man page Man page
getForegroundSE	Man page
getForegroundSE,GenePixData-method	Man page
getForegroundSE,SpotData-method	Man page
getForegroundSE.GenePixData	Man page Man page
getForegroundSE.SpotData	Man page Man page
getForegroundSNR	Man page
getForegroundSNR.QuantArrayData	Man page
getG	Man page
getG.MAData	Man page
getGene	Man page
getGene.Replicates	Man page
getGeneDiscrepancies	Man page
getGeneDiscrepancies.MAData	Man page
getGeneGroups	Man page
getGeneGroups.Layout	Man page
getGeneIndex	Man page
getGeneIndex.Layout	Man page
getGeneReplicateIndex	Man page
getGeneReplicateIndex.Layout	Man page
getGeneReplicateSlideValues	Man page
getGeneReplicateSlideValues.GeneReplicateSlideArray	Man page
getGeneReplicateSlideValues.GeneSlideArray	Man page
getGeneReplicateSlideValues.MicroarrayArray	Man page
getGeneReplicateSlideValues.SpotSlideArray	Man page
getGeneReplicateSlideValues.default	Man page
getGeneResiduals	Man page
getGeneResiduals.MAData	Man page
getGeneSlideReplicateIndex	Man page
getGeneSlideReplicateIndex,MicroarrayData-method	Man page
getGeneSlideReplicateIndex.MicroarrayData	Man page Man page
getGeneSlideValues	Man page
getGeneSlideValues.GeneReplicateSlideArray	Man page
getGeneSlideValues.GeneSlideArray	Man page
getGeneSlideValues.MicroarrayArray	Man page
getGeneSlideValues.SpotSlideArray	Man page
getGeneSlideValues.default	Man page
getGeneVariability	Man page
getGeneVariability,MAData-method	Man page
getGeneVariability.MAData	Man page Man page
getGenewiseResiduals	Man page
getGenewiseResiduals.MAData	Man page
getGrid	Man page
getGrid.ScanAlyze20Data	Man page
getGrid.ScanAlyzeData	Man page
getGridColumn	Man page
getGridColumn.GalLayout	Man page
getGridRow	Man page
getGridRow.GalLayout	Man page
getGroupValues	Man page
getGroupValues.LayoutGroups	Man page
getGroups	Man page
getGroups.SuperGroups	Man page
getHeaderField	Man page
getHeaderField.GenePixData	Man page
getHeaderFields	Man page
getHeaderFields.GenePixData	Man page
getHistogram	Man page
getHistogram.MAData	Man page
getID	Man page
getID.Layout	Man page
getId	Man page
getId,Layout-method	Man page
getId.Layout	Man page Man page
getImageSoftwaresUsed	Man page
getImageSoftwaresUsed.ExperimentalSetup	Man page
getInclude	Man page
getInclude.MicroarrayData	Man page
getIndex	Man page
getIndex,AcceptFilter-method	Man page
getIndex,AndFilter-method	Man page
getIndex,FieldFilter-method	Man page
getIndex,Filter-method	Man page
getIndex,Layout-method	Man page
getIndex,OrFilter-method	Man page
getIndex.AcceptFilter	Man page Man page
getIndex.AndFilter	Man page Man page
getIndex.FieldFilter	Man page Man page
getIndex.Filter	Man page Man page
getIndex.GeneAcceptFilter	Man page
getIndex.GeneRejectFilter	Man page
getIndex.Layout	Man page Man page
getIndex.NotFilter	Man page
getIndex.OrFilter	Man page Man page
getIndex.RejectFilter	Man page
getIndex0	Man page
getIndex0.FieldFilter	Man page
getIndices	Man page
getIndices,Layout-method	Man page
getIndices.Layout	Man page Man page
getInput	Man page
getInput,Filter-method	Man page
getInput,ParallelFilter-method	Man page
getInput,SerialFilter-method	Man page
getInput.Filter	Man page Man page
getInput.ParallelFilter	Man page Man page
getInput.SerialFilter	Man page Man page
getKnownHeadersWithType	Man page
getKnownHeadersWithType.GenePixData	Man page
getKnownHeadersWithType.ScanAlyze20Data	Man page
getKnownHeadersWithType.ScanAlyzeData	Man page
getLabel	Man page
getLabel,MicroarrayData-method	Man page
getLabel.MicroarrayData	Man page Man page
getLaserOnTime	Man page
getLaserOnTime.GenePixData	Man page
getLaserPower	Man page
getLaserPower.GenePixData	Man page
getLast	Man page
getLast.PlateGroups	Man page
getLayout	Man page
getLayout,MicroarrayData-method	Man page
getLayout.LayoutGroups	Man page
getLayout.MicroarrayArray	Man page
getLayout.MicroarrayData	Man page Man page
getLayoutFiles	Man page
getLayoutFiles.ExperimentalSetup	Man page
getLayoutGroupsByName	Man page
getLayoutGroupsByName.Layout	Man page
getLeftEdge	Man page
getLeftEdge,SpotPosition-method	Man page
getLeftEdge.SpotPosition	Man page Man page
getLinesAveraged	Man page
getLinesAveraged.GenePixData	Man page
getLocation	Man page
getLocation,Layout-method	Man page
getLocation.Layout	Man page Man page
getLogIntensities	Man page
getLogIntensities,RGData-method	Man page
getLogIntensities.RGData	Man page Man page
getLogRatios	Man page
getLogRatios,RGData-method	Man page
getLogRatios.RGData	Man page Man page
getM	Man page
getM.RGData	Man page
getMOR	Man page
getMOR,MAData-method	Man page
getMOR.MAData	Man page Man page
getMOR2003a	Man page
getMOR2003a,MAData-method	Man page
getMOR2003a.MAData	Man page Man page
getMaxHeight	Man page
getMaxHeight,SpotPosition-method	Man page
getMaxHeight.SpotPosition	Man page Man page
getMaxWidth	Man page
getMaxWidth,SpotPosition-method	Man page
getMaxWidth.SpotPosition	Man page Man page
getName,Layout-method	Man page
getName.Layout	Man page Man page
getNames	Man page
getNames,GeneGroups-method	Man page
getNames.GeneGroups	Man page Man page
getNames.LayoutGroups	Man page
getNames.PlateGroups	Man page
getNames.PrintdipGroups	Man page
getNames.PrinttipGroups	Man page
getNames.SlideColumnGroups	Man page
getNames.SlideRowGroups	Man page
getNames.SuperGroups	Man page
getNotFound	Man page
getNotFound.GenePixData	Man page
getPMTGain	Man page
getPMTGain.GenePixData	Man page
getPValues	Man page
getPValues.TMAData	Man page
getParameter	Man page
getParameter,Filter-method	Man page
getParameter.Filter	Man page Man page
getParameter.Replicates	Man page
getPerimeter	Man page
getPerimeter.SpotData	Man page
getPerimeter.SpotfinderData	Man page
getPixelSize	Man page
getPixelSize.GenePixData	Man page
getPlate	Man page
getPlate.Layout	Man page
getPlateGroups	Man page
getPlateGroups.Layout	Man page
getPlateNumber	Man page
getPlateNumber.Layout	Man page
getPosition,Layout-method	Man page
getPosition.Layout	Man page Man page
getPrintdipGroups	Man page
getPrintdipGroups.Layout	Man page
getPrintorder	Man page
getPrintorder,Layout-method	Man page
getPrintorder.Layout	Man page Man page
getPrintorderIndices	Man page
getPrintorderIndices.PlateGroups	Man page
getPrinttipGroups	Man page
getPrinttipGroups.Layout	Man page
getProbeWeights	Man page
getProbeWeights.MicroarrayData	Man page
getQuadruplicates	Man page
getQuadruplicates,GeneGroups-method	Man page
getQuadruplicates.GeneGroups	Man page Man page
getR	Man page
getR.MAData	Man page
getRange	Man page
getRange.MAData	Man page
getRawData	Man page
getRawData,GenePixData-method	Man page
getRawData,ImaGeneData-method	Man page
getRawData,QuantArrayData-method	Man page
getRawData,ScanAlyzeData-method	Man page
getRawData,SpotData-method	Man page
getRawData,SpotfinderData-method	Man page
getRawData.GenePixData	Man page Man page
getRawData.ImaGeneData	Man page Man page
getRawData.QuantArrayData	Man page Man page
getRawData.ScanAlyzeData	Man page Man page
getRawData.SpotData	Man page Man page
getRawData.SpotfinderData	Man page Man page
getReplicates	Man page
getReplicates,GeneGroups-method	Man page
getReplicates.GeneGroups	Man page Man page
getReplicates.Layout	Man page
getRgn R2	Man page
getRgn R2.GenePixData	Man page
getRightEdge	Man page
getRightEdge,SpotPosition-method	Man page
getRightEdge.SpotPosition	Man page Man page
getRow	Man page
getRow.GalLayout	Man page
getSE	Man page
getSE.TMAData	Man page
getSNR	Man page
getSNR.SpotData	Man page
getSNR.SpotfinderData	Man page
getSNR1	Man page
getSNR1.RawData	Man page
getSNR2	Man page
getSNR2.RawData	Man page
getSampleUsed	Man page
getSampleUsed.ExperimentalSetup	Man page
getScannersUsed	Man page
getScannersUsed.ExperimentalSetup	Man page
getSignal	Man page
getSignal,RawData-method	Man page
getSignal.RawData	Man page Man page
getSignalWeights	Man page
getSignalWeights.MicroarrayData	Man page
getSizes	Man page
getSizes,GeneGroups-method	Man page
getSizes.GeneGroups	Man page Man page
getSizes.PlateGroups	Man page
getSizes.PrintdipGroups	Man page
getSizes.PrinttipGroups	Man page
getSizes.SlideColumnGroups	Man page
getSizes.SlideRowGroups	Man page
getSizes.SuperGroups	Man page
getSlide	Man page
getSlide.MAData	Man page
getSlideColumnGroups	Man page
getSlideColumnGroups.Layout	Man page
getSlideName	Man page
getSlideName.MicroarrayData	Man page
getSlideNames	Man page
getSlideNames,MicroarrayData-method	Man page
getSlideNames.MicroarrayData	Man page Man page
getSlidePairs	Man page
getSlidePairs.MicroarrayData	Man page
getSlideRowGroups	Man page
getSlideRowGroups.Layout	Man page
getSpot	Man page
getSpot.Replicates	Man page
getSpotColumn	Man page
getSpotColumn.ScanAlyze20Data	Man page
getSpotColumn.ScanAlyzeData	Man page
getSpotIndex	Man page
getSpotIndex.Layout	Man page
getSpotOrGeneSlideValues	Man page
getSpotOrGeneSlideValues.GeneReplicateSlideArray	Man page
getSpotOrGeneSlideValues.GeneSlideArray	Man page
getSpotOrGeneSlideValues.MicroarrayArray	Man page
getSpotOrGeneSlideValues.SpotSlideArray	Man page
getSpotPosition	Man page
getSpotPosition,GenePixData-method	Man page
getSpotPosition,ImaGeneData-method	Man page
getSpotPosition,QuantArrayData-method	Man page
getSpotPosition,ScanAlyze20Data-method	Man page
getSpotPosition,ScanAlyzeData-method	Man page
getSpotPosition,SpotData-method	Man page
getSpotPosition.GenePixData	Man page Man page
getSpotPosition.ImaGeneData	Man page Man page
getSpotPosition.MicroarrayData	Man page
getSpotPosition.QuantArrayData	Man page Man page
getSpotPosition.ScanAlyze20Data	Man page Man page
getSpotPosition.ScanAlyzeData	Man page Man page
getSpotPosition.SpotData	Man page Man page
getSpotRow	Man page
getSpotRow.ScanAlyze20Data	Man page
getSpotRow.ScanAlyzeData	Man page
getSpotSlideValues	Man page
getSpotSlideValues.GeneReplicateSlideArray	Man page
getSpotSlideValues.GeneSlideArray	Man page
getSpotSlideValues.MicroarrayArray	Man page
getSpotSlideValues.SpotSlideArray	Man page
getSpotSlideValues.default	Man page
getSpotValue	Man page
getSpotValue.MicroarrayData	Man page
getSpotValues	Man page
getSpotValues.LayoutGroups	Man page
getSpotVariability	Man page
getSpotVariability.MAData	Man page
getSpots	Man page
getSpots,GeneGroups-method	Man page
getSpots.GeneGroups	Man page Man page
getSpots.LayoutGroups	Man page
getSpots.PlateGroups	Man page
getSpots.PrintdipGroups	Man page
getSpots.PrinttipGroups	Man page
getSpots.SlideColumnGroups	Man page
getSpots.SlideRowGroups	Man page
getSpots.SuperGroups	Man page
getStandardError	Man page
getStandardError.TMAData	Man page
getTemperature	Man page
getTemperature.GenePixData	Man page
getTopEdge	Man page
getTopEdge,SpotPosition-method	Man page
getTopEdge.SpotPosition	Man page Man page
getTreatments	Man page
getTreatments.MicroarrayData	Man page
getTriplicates	Man page
getTriplicates,GeneGroups-method	Man page
getTriplicates.GeneGroups	Man page Man page
getView	Man page
getView.GeneReplicateSlideArray	Man page
getView.GeneSlideArray	Man page
getView.MicroarrayArray	Man page
getView.MicroarrayData	Man page
getView.SpotSlideArray	Man page
getView.default	Man page
getVisible	Man page
getVisible,Filter-method	Man page
getVisible.Filter	Man page Man page
getWavelengths	Man page
getWavelengths.GenePixData	Man page
getWeights	Man page
getWeights.MicroarrayData	Man page
getWeightsAsString	Man page
getWeightsAsString.MicroarrayData	Man page
getWithinChannelPairs	Man page
getWithinChannelPairs.RGData	Man page
getWithinChannelPairs.RawData	Man page
gridSize	Man page
gridSize,Layout-method	Man page
gridSize.Layout	Man page Man page
hasBootstrap	Man page
hasBootstrap.AffineModelFit	Man page
hasExcludedSpots	Man page
hasExcludedSpots.MicroarrayData	Man page
hasIDs	Man page
hasIDs.Layout	Man page
hasIds	Man page
hasIds.Layout	Man page
hasLayout	Man page
hasLayout,MicroarrayData-method	Man page
hasLayout.MicroarrayData	Man page Man page
hasNames	Man page
hasNames.Layout	Man page
hasPlates	Man page
hasPlates.Layout	Man page
hasProbeWeights	Man page
hasProbeWeights.MicroarrayData	Man page
hasReplicates	Man page
hasReplicates.Layout	Man page
hasReplicates.Replicates	Man page
hasSignalWeights	Man page
hasSignalWeights.MicroarrayData	Man page
hasWeights	Man page
hasWeights.MicroarrayData	Man page
highlight	Man page
highlight,Filter-method	Man page
highlight,MicroarrayData-method	Man page
highlight.Filter	Man page Man page
highlight.MicroarrayData	Man page Man page
highlight.Replicates	Man page
hist,MicroarrayData-method	Man page
hist.MAData	Man page
hist.MicroarrayData	Man page Man page
indexOf	Man page
indexOf,Layout-method	Man page
indexOf.Layout	Man page Man page
is.above	Man page
is.above.default	Man page
isFieldColorable	Man page
isFieldColorable.MicroarrayData	Man page
isSaturated	Man page
isSaturated,MicroarrayData-method	Man page
isSaturated.MicroarrayData	Man page Man page
keepSlides	Man page
keepSlides,MicroarrayData-method	Man page
keepSlides.MicroarrayData	Man page Man page
keepSpots	Man page
keepSpots,MicroarrayData-method	Man page
keepSpots.MicroarrayData	Man page Man page
listFlags	Man page
listFlags,MicroarrayData-method	Man page
listFlags.MicroarrayData	Man page Man page
listToMatrix	Man page
listToMatrix.default	Man page
lmGenewise	Man page
lmGenewise.Analyzer	Man page
loadData	Man page
loadData.SMA	Man page
loessQuantile	Man page
loessQuantile,MAData-method	Man page
loessQuantile.MAData	Man page Man page
log	Man page
log.RGData	Man page
log.SpotData	Man page
log.default	Man page
log.na	Man page
logPreferred	Man page
logPreferred.SpotData	Man page
lowessCurve	Man page
lowessCurve,MicroarrayData-method	Man page
lowessCurve.MicroarrayData	Man page Man page
lowessLine	Man page
lowessLine.MicroarrayData	Man page
mad	Man page
mad.MultiwayArray	Man page
mad.default	Man page
matrixToList	Man page
matrixToList.default	Man page
mean,MAData-method	Man page
mean,RGData-method	Man page
mean.MAData	Man page Man page
mean.MultiwayArray	Man page
mean.RGData	Man page Man page
median	Man page
median.MultiwayArray	Man page
median.default	Man page
nbrOfColumns	Man page
nbrOfColumns,Layout-method	Man page
nbrOfColumns.Layout	Man page Man page
nbrOfDataPoints	Man page
nbrOfDataPoints.MicroarrayData	Man page
nbrOfDimensions	Man page
nbrOfDimensions.MultiwayArray	Man page
nbrOfFields	Man page
nbrOfFields,MicroarrayData-method	Man page
nbrOfFields.GalLayout	Man page
nbrOfFields.MicroarrayData	Man page Man page
nbrOfGenes	Man page
nbrOfGenes.Replicates	Man page
nbrOfGrids	Man page
nbrOfGrids,Layout-method	Man page
nbrOfGrids.Layout	Man page Man page
nbrOfGroups	Man page
nbrOfGroups,GeneGroups-method	Man page
nbrOfGroups.GeneGroups	Man page Man page
nbrOfGroups.LayoutGroups	Man page
nbrOfGroups.PlateGroups	Man page
nbrOfGroups.PrintdipGroups	Man page
nbrOfGroups.PrinttipGroups	Man page
nbrOfGroups.SlideColumnGroups	Man page
nbrOfGroups.SlideRowGroups	Man page
nbrOfGroups.SuperGroups	Man page
nbrOfHybridizations	Man page
nbrOfHybridizations.ExperimentalSetup	Man page
nbrOfPlates	Man page
nbrOfPlates.Layout	Man page
nbrOfReplicates	Man page
nbrOfReplicates.Layout	Man page
nbrOfReplicates.Replicates	Man page
nbrOfRows	Man page
nbrOfRows,Layout-method	Man page
nbrOfRows.Layout	Man page Man page
nbrOfSlides	Man page
nbrOfSlides,MicroarrayData-method	Man page
nbrOfSlides,SpotPosition-method	Man page
nbrOfSlides.MicroarrayData	Man page Man page
nbrOfSlides.SpotPosition	Man page Man page
nbrOfSpots	Man page
nbrOfSpots,Layout-method	Man page
nbrOfSpots,MicroarrayData-method	Man page
nbrOfSpots,SpotPosition-method	Man page
nbrOfSpots.Layout	Man page Man page
nbrOfSpots.MicroarrayData	Man page Man page
nbrOfSpots.Replicates	Man page
nbrOfSpots.SpotPosition	Man page Man page
nbrOfTreatments	Man page
nbrOfTreatments.MicroarrayData	Man page
ncol.GeneReplicateSlideArray	Man page
ncol.GeneSlideArray	Man page
normalizeAcrossSlides	Man page
normalizeAcrossSlides,MAData-method	Man page
normalizeAcrossSlides.MAData	Man page Man page
normalizeAffine	Man page
normalizeAffine,MAData-method	Man page
normalizeAffine,RGData-method	Man page
normalizeAffine.MAData	Man page Man page
normalizeAffine.RGData	Man page Man page
normalizeAffine.RawData	Man page
normalizeAffineShift	Man page
normalizeAffineShift,MAData-method	Man page
normalizeAffineShift.MAData	Man page Man page
normalizeCurveFit	Man page
normalizeCurveFit,MAData-method	Man page
normalizeCurveFit,RGData-method	Man page
normalizeCurveFit.MAData	Man page Man page
normalizeCurveFit.RGData	Man page Man page
normalizeGenewise	Man page
normalizeGenewise.GenePixData	Man page
normalizeGenewise.MAData	Man page
normalizeGenewise.MicroarrayData	Man page
normalizeGenewise.RGData	Man page
normalizeGenewise.RawData	Man page
normalizeGenewise.ScanAlyzeData	Man page
normalizeGenewise.SpotData	Man page
normalizeGenewise.SpotfinderData	Man page
normalizeGroupsConstant	Man page
normalizeGroupsConstant.MicroarrayData	Man page
normalizeGroupsShiftFunction	Man page
normalizeGroupsShiftFunction.MicroarrayData	Man page
normalizeLoess	Man page
normalizeLoess.RGData	Man page
normalizeLogRatioShift	Man page
normalizeLogRatioShift,MAData-method	Man page
normalizeLogRatioShift.MAData	Man page Man page
normalizeLowess	Man page
normalizeLowess.RGData	Man page
normalizePlatewise	Man page
normalizePlatewise,MicroarrayData-method	Man page
normalizePlatewise.MAData	Man page
normalizePlatewise.MicroarrayData	Man page Man page
normalizePrintorder	Man page
normalizePrintorder.MAData	Man page
normalizePrintorder.MicroarrayData	Man page
normalizeQuantile	Man page
normalizeQuantile.MAData	Man page
normalizeQuantile.MicroarrayData	Man page
normalizeQuantile.RGData	Man page
normalizeQuantile.RawData	Man page
normalizeRobustSpline	Man page
normalizeRobustSpline.RGData	Man page
normalizeSpatial	Man page
normalizeSpatial.MAData	Man page
normalizeSpatial.MicroarrayData	Man page
normalizeSpline	Man page
normalizeSpline.RGData	Man page
normalizeWithinSlide	Man page
normalizeWithinSlide,MAData-method	Man page
normalizeWithinSlide.MAData	Man page Man page
normalizeWithinSlide.RawData	Man page
nrow.GeneReplicateSlideArray	Man page
nrow.GeneSlideArray	Man page
plot,MicroarrayData-method	Man page
plot,SpotPosition-method	Man page
plot.MAData	Man page
plot.MicroarrayData	Man page Man page
plot.RGData	Man page
plot.RawData	Man page
plot.SpotPosition	Man page Man page
plot.TMAData	Man page
plot3d.MAData	Man page
plot3d.MicroarrayData	Man page
plotDensity	Man page
plotDensity,MicroarrayData-method	Man page
plotDensity.MAData	Man page
plotDensity.MicroarrayData	Man page Man page
plotDiporder	Man page
plotDiporder.MAData	Man page
plotDiporder.MicroarrayData	Man page
plotGene	Man page
plotGene.MicroarrayData	Man page
plotMvsA	Man page
plotMvsAPairs	Man page
plotMvsM	Man page
plotMvsM,MAData-method	Man page
plotMvsM.MAData	Man page Man page
plotMvsMPairs	Man page
plotPrintorder	Man page
plotPrintorder,MicroarrayData-method	Man page
plotPrintorder.MAData	Man page
plotPrintorder.MicroarrayData	Man page Man page
plotPrintorder.TMAData	Man page
plotReplicates	Man page
plotReplicates.MicroarrayData	Man page
plotSpatial	Man page
plotSpatial,GenePixData-method	Man page
plotSpatial,MicroarrayData-method	Man page
plotSpatial,QuantArrayData-method	Man page
plotSpatial,ScanAlyzeData-method	Man page
plotSpatial,SpotData-method	Man page
plotSpatial,SpotfinderData-method	Man page
plotSpatial.GenePixData	Man page Man page
plotSpatial.ImaGeneData	Man page
plotSpatial.MAData	Man page
plotSpatial.MicroarrayData	Man page Man page
plotSpatial.QuantArrayData	Man page Man page
plotSpatial.RGData	Man page
plotSpatial.RawData	Man page
plotSpatial.ScanAlyzeData	Man page Man page
plotSpatial.SpotData	Man page Man page
plotSpatial.SpotfinderData	Man page Man page
plotSpatial.TMAData	Man page
plotSpatial3d	Man page
plotSpatial3d,MicroarrayData-method	Man page
plotSpatial3d.GenePixData	Man page
plotSpatial3d.ImaGeneData	Man page
plotSpatial3d.MAData	Man page
plotSpatial3d.MicroarrayData	Man page Man page
plotSpatial3d.QuantArrayData	Man page
plotSpatial3d.ScanAlyzeData	Man page
plotSpatial3d.SpotData	Man page
plotSpatial3d.SpotfinderData	Man page
plotTTest	Man page
plotTTest.Analyzer	Man page
plotXY	Man page
plotXY,MicroarrayData-method	Man page
plotXY.BMAData	Man page
plotXY.MAData	Man page
plotXY.MicroarrayData	Man page Man page
plotXY.RGData	Man page
plotXY.RawData	Man page
plotXY.SSMatrix	Man page
plotXY.TMAData	Man page
points,SpotPosition-method	Man page
points.MicroarrayData	Man page
points.SpotPosition	Man page Man page
popView	Man page
popView.MicroarrayArray	Man page
popView.default	Man page
power	Man page
power.RGData	Man page
power.default	Man page
preferredLogBase	Man page
preferredLogBase.SpotData	Man page
print.AffineModelFit	Man page
print.ExperimentalSetup	Man page
print.MultiwayArray	Man page
prod	Man page
prod.MultiwayArray	Man page
prod.default	Man page
projectUontoV	Man page
pushView	Man page
pushView.MicroarrayArray	Man page
pushView.default	Man page
put	Man page
put.Layout	Man page
putGene	Man page
putGene.MicroarrayData	Man page
putSlide	Man page
putSlide.MicroarrayData	Man page
qqnorm.MAData	Man page
qqnorm.MicroarrayData	Man page
qqplotTTest	Man page
qqplotTTest.Analyzer	Man page
quantile.MicroarrayData	Man page
range.MAData	Man page
range.MicroarrayData	Man page
range.RGData	Man page
range.RawData	Man page
range2	Man page
range2.MicroarrayData	Man page
read,ExperimentalSetup-method	Man page
read,GalLayout-method	Man page
read,GenePixData-method	Man page
read,ImaGeneData-method	Man page
read,Layout-method	Man page
read,MicroarrayData-method	Man page
read,QuantArrayData-method	Man page
read,ScanAlyze20Data-method	Man page
read,ScanAlyzeData-method	Man page
read,SpotData-method	Man page
read,SpotfinderData-method	Man page
read.ExperimentalSetup	Man page Man page
read.GalLayout	Man page Man page
read.GenePixData	Man page Man page
read.ImaGeneData	Man page Man page
read.Layout	Man page Man page
read.MAData	Man page
read.MicroarrayData	Man page Man page
read.QuantArrayData	Man page Man page
read.RGData	Man page
read.RawData	Man page
read.ScanAlyze20Data	Man page Man page
read.ScanAlyzeData	Man page Man page
read.SpotData	Man page Man page
read.SpotPosition	Man page
read.SpotfinderData	Man page Man page
read.table	Man page
read.table.QuantArrayData	Man page
read.table.default	Man page
readAll	Man page
readAll.GenePixData	Man page
readAll.QuantArrayData	Man page
readAll.ScanAlyzeData	Man page
readAll.SpotData	Man page
readHeader	Man page
readHeader,GenePixData-method	Man page
readHeader.GenePixData	Man page Man page
readHeader.MicroarrayData	Man page
readInternal	Man page
readInternal.ScanAlyze20Data	Man page
readInternal.ScanAlyzeData	Man page
readInternalSafe	Man page
readInternalSafe.ScanAlyzeData	Man page
readOneFile	Man page
readOneFile,QuantArrayData-method	Man page
readOneFile,SpotfinderData-method	Man page
readOneFile.GenePixData	Man page
readOneFile.QuantArrayData	Man page Man page
readOneFile.ScanAlyzeData	Man page
readOneFile.SpotData	Man page
readOneFile.SpotfinderData	Man page Man page
readToList	Man page
readToList.MicroarrayData	Man page
removeSlides	Man page
removeSlides,MicroarrayData-method	Man page
removeSlides.MicroarrayData	Man page Man page
removeSpots	Man page
removeSpots,MicroarrayData-method	Man page
removeSpots.MicroarrayData	Man page Man page
rename	Man page
rename.Layout	Man page
renameFields	Man page
renameFields.SpotData	Man page
resetProbeWeights	Man page
resetProbeWeights.MicroarrayData	Man page
resetSignalWeights	Man page
resetSignalWeights.MicroarrayData	Man page
residuals.AffineModelFit	Man page
rotate	Man page
rotate.Matrix	Man page
rowAverages	Man page
rowAverages.matrix	Man page
scalarProduct	Man page
select	Man page
select,MicroarrayData-method	Man page
select.MicroarrayData	Man page Man page
seq.LayoutGroups	Man page
seq.MicroarrayData	Man page
set,Layout-method	Man page
set.Layout	Man page Man page
set.MicroarrayData	Man page
set.Replicates	Man page
setByLayout	Man page
setByLayout.Layout	Man page
setCache	Man page
setCache.MicroarrayData	Man page
setDesignMatrix	Man page
setDesignMatrix.Analyzer	Man page
setExcludedSpots	Man page
setExcludedSpots.MicroarrayData	Man page
setExplicit	Man page
setExplicit.Layout	Man page
setExtra	Man page
setExtra,MicroarrayData-method	Man page
setExtra.MicroarrayData	Man page Man page
setField	Man page
setField.MAData	Man page
setField.MicroarrayData	Man page
setField.RGData	Man page
setField.RawData	Man page
setFlag	Man page
setFlag,MicroarrayData-method	Man page
setFlag.MicroarrayData	Man page Man page
setGeneGroups	Man page
setGeneGroups.Layout	Man page
setGeneReplicateSlideValues	Man page
setGeneReplicateSlideValues.MicroarrayArray	Man page
setGeneSlideValues	Man page
setGeneSlideValues.GeneSlideArray	Man page
setGeneSlideValues.MicroarrayArray	Man page
setGroups	Man page
setGroups.SuperGroups	Man page
setHeaderField	Man page
setHeaderField.GenePixData	Man page
setID	Man page
setID.Layout	Man page
setId	Man page
setId,Layout-method	Man page
setId.Layout	Man page Man page
setLabel	Man page
setLabel,MicroarrayData-method	Man page
setLabel.MicroarrayData	Man page Man page
setLayout	Man page
setLayout,MicroarrayData-method	Man page
setLayout.GenePixData	Man page
setLayout.ImaGeneData	Man page
setLayout.LayoutGroups	Man page
setLayout.MicroarrayData	Man page Man page
setLayout.QuantArrayData	Man page
setName	Man page
setName,Layout-method	Man page
setName.Layout	Man page Man page
setParameter	Man page
setParameter,Filter-method	Man page
setParameter.Filter	Man page Man page
setParameter.Replicates	Man page
setPlate	Man page
setPlate.Layout	Man page
setPlateGroups	Man page
setPlateGroups.Layout	Man page
setPrintdipGroups	Man page
setPrintdipGroups.Layout	Man page
setPrintorder	Man page
setPrintorder.Layout	Man page
setPrinttipGroups	Man page
setPrinttipGroups.Layout	Man page
setProbeWeights	Man page
setProbeWeights,MicroarrayData-method	Man page
setProbeWeights.MicroarrayData	Man page Man page
setReplicates	Man page
setReplicates.Layout	Man page
setSaturated	Man page
setSaturated,MicroarrayData-method	Man page
setSaturated.MicroarrayData	Man page Man page
setSignalWeights	Man page
setSignalWeights.MicroarrayData	Man page
setSlideColumnGroups	Man page
setSlideColumnGroups.Layout	Man page
setSlideName	Man page
setSlideName.MicroarrayData	Man page
setSlideNames	Man page
setSlideNames,MicroarrayData-method	Man page
setSlideNames.MicroarrayData	Man page Man page
setSlideRowGroups	Man page
setSlideRowGroups.Layout	Man page
setSpotSlideValues	Man page
setSpotSlideValues.MicroarrayArray	Man page
setSpotSlideValues.SpotSlideArray	Man page
setTreatments	Man page
setTreatments.MicroarrayData	Man page
setView	Man page
setView.MicroarrayArray	Man page
setView.MicroarrayData	Man page
setVisible	Man page
setVisible,Filter-method	Man page
setVisible.Filter	Man page Man page
setWeights	Man page
setWeights.MicroarrayData	Man page
shift	Man page
shift,MAData-method	Man page
shift,RGData-method	Man page
shift,RawData-method	Man page
shift.MAData	Man page Man page
shift.RGData	Man page Man page
shift.RawData	Man page Man page
shiftEqualRG	Man page
shiftEqualRG.MAData	Man page
size,Layout-method	Man page
size,MicroarrayData-method	Man page
size,SpotPosition-method	Man page
size.Layout	Man page Man page
size.MicroarrayData	Man page Man page
size.SpotPosition	Man page Man page
str,MicroarrayData-method	Man page
str.MicroarrayArray	Man page
str.MicroarrayData	Man page Man page
str.Replicates	Man page
subplots,MicroarrayData-method	Man page
subplots.MicroarrayData	Man page Man page
sum	Man page
sum.MultiwayArray	Man page
sum.default	Man page
summary,MicroarrayData-method	Man page
summary.AffineModelFit	Man page
summary.MicroarrayData	Man page Man page
swapDyes	Man page
swapDyes,MAData-method	Man page
swapDyes,RGData-method	Man page
swapDyes,RawData-method	Man page
swapDyes.MAData	Man page Man page
swapDyes.RGData	Man page Man page
swapDyes.RawData	Man page Man page
text,Filter-method	Man page
text,MicroarrayData-method	Man page
text.Filter	Man page Man page
text.MicroarrayData	Man page Man page
text.Replicates	Man page
toPrintorderMatrix	Man page
toPrintorderMatrix,Layout-method	Man page
toPrintorderMatrix.Layout	Man page Man page
toXYMatrix	Man page
toXYMatrix,Layout-method	Man page
toXYMatrix.Layout	Man page Man page
topSpots	Man page
topSpots,MAData-method	Man page
topSpots.MAData	Man page Man page
topSpots.TMAData	Man page
tr	Man page
ttest	Man page
ttest.Analyzer	Man page
unite	Man page
unite,MicroarrayWeights-method	Man page
unite.MicroarrayWeights	Man page Man page
unloadData	Man page
unloadData.SMA	Man page
updateHeader	Man page
updateHeader.ImaGeneData	Man page
updateHeader.MicroarrayData	Man page
validateArgumentChannel	Man page
validateArgumentChannel.MicroarrayData	Man page
validateArgumentChannels	Man page
validateArgumentChannels,GenePixData-method	Man page
validateArgumentChannels.GenePixData	Man page Man page
validateArgumentChannels.MicroarrayData	Man page
validateArgumentFileAndPath	Man page
validateArgumentFileAndPath.File	Man page
validateArgumentGroupBy	Man page
validateArgumentGroupBy,MicroarrayData-method	Man page
validateArgumentGroupBy.MicroarrayData	Man page Man page
validateArgumentSlide	Man page
validateArgumentSlide,MicroarrayData-method	Man page
validateArgumentSlide.MicroarrayData	Man page Man page
validateArgumentSlides	Man page
validateArgumentSlides,MicroarrayData-method	Man page
validateArgumentSlides.MicroarrayData	Man page Man page
validateArgumentSpotIndex	Man page
validateArgumentSpotIndex.MicroarrayData	Man page
validateArgumentWeights	Man page
validateArgumentWeights,MicroarrayData-method	Man page
validateArgumentWeights.MicroarrayData	Man page Man page
var	Man page
var,MAData-method	Man page
var,RGData-method	Man page
var.MAData	Man page Man page
var.MultiwayArray	Man page
var.RGData	Man page Man page
var.default	Man page
write,GenePixData-method	Man page
write,ImaGeneData-method	Man page
write,Layout-method	Man page
write,MicroarrayData-method	Man page
write,QuantArrayData-method	Man page
write,ScanAlyze20Data-method	Man page
write,ScanAlyzeData-method	Man page
write,SpotData-method	Man page
write,SpotPosition-method	Man page
write,SpotfinderData-method	Man page
write.GalLayout	Man page
write.GenePixData	Man page Man page
write.ImaGeneData	Man page Man page
write.Layout	Man page Man page
write.MicroarrayData	Man page Man page
write.QuantArrayData	Man page Man page
write.ScanAlyze20Data	Man page Man page
write.ScanAlyzeData	Man page Man page
write.SpotData	Man page Man page
write.SpotPosition	Man page Man page
write.SpotfinderData	Man page Man page
writeHeader	Man page
writeHeader.MicroarrayData	Man page