averagePixels	readBeadLevelData
backgroundCorrect	backgroundCorrect
backgroundCorrect,BeadLevelList-method	backgroundCorrect
backgroundCorrect,BeadLevelList-methods	backgroundCorrect
backgroundNormalise	backgroundNormalise
backgroundNormalise, ExpressionSetIllumina, ExpressionSetIllumina-method	class.ExpressionSetIllumina
backgroundNormalise, ExpressionSetIllumina-method	backgroundNormalise
backgroundNormalise, ExpressionSetIllumina-methods	class.ExpressionSetIllumina
BeadChipSummary	interactivePlots
BeadLevelList-class	class-BeadLevelList
BeadLevelNormalise	BeadLevelNormalise
BLData	BLData
BSData	BSData
calculateBackground	readBeadLevelData
calculateForegroundIntensities	readBeadLevelData
cbind.BeadLevelList	cbind
class:ExpressionSetIllumina	class.ExpressionSetIllumina
combine,ExpressionSetIllumina,ANY-method	class.ExpressionSetIllumina
combine,ExpressionSetIllumina,ExpressionSetIllumina-method	class.ExpressionSetIllumina
createBeadSummaryData	createBeadSummaryData
createBeadSummaryData, BeadLevelList-method	findBeadStatus
createBeadSummaryData,BeadLevelList-method	createBeadSummaryData
createBeadSummaryDataSlow	createBeadSummaryData
Detection	class.ExpressionSetIllumina
Detection,ExpressionSetIllumina-method	class.ExpressionSetIllumina
DiffScore	DiffScore
dim.BeadLevelList	dim
dimnames.BeadLevelList	dimnames
displayTIFFImage	displayTIFFImage
ExpressionSetIllumina-class	class.ExpressionSetIllumina
exprs,ExpressionSetIllumina-method	class.ExpressionSetIllumina
exprs<-,ExpressionSetIllumina,matrix-method	class.ExpressionSetIllumina
findAllOutliers	findAllOutliers
findAllOutliers, BeadLevelList-method	findBeadStatus
findAllOutliersSlow	findAllOutliers
findBeadStatus	findBeadStatus
FindIlluminaSpotl	displayTIFFImage
getProbeIndices	findBeadStatus
getProbeIndicesC	findBeadStatus
getProbeIntensities	findBeadStatus
getProbeIntensities,BeadLevelList-method	findBeadStatus
IdentifyBeads	displayTIFFImage
IdentifyIntensity	displayTIFFImage
imageplot	imageplot
imageplot, BeadLevelList-methods	class-BeadLevelList
initialize,BeadLevelList-method	class-BeadLevelList
initialize,ExpressionSetIllumina-method	class.ExpressionSetIllumina
LargeDataObject-class	LargeDataObject
medianNormalise	medianNormalise
NoBeads	class.ExpressionSetIllumina
NoBeads,ExpressionSetIllumina-method	class.ExpressionSetIllumina
plotBeadIntensities	plotBeadIntensities
plotBeadLocations	plotBeadLocations
plotMA	plotMA
plotMAXY	plotMAXY
plotOnSAM	plotOnSAM
plotQC	readQC
plotQC.figure1	readQC
plotQC.figure2	readQC
plotQC.figure3	readQC
plotQC.figure4	readQC
plotQC.figure5	readQC
plotQC.figure6	readQC
plotXY	plotXY
print.BeadLevelList	class-BeadLevelList
QC	QC
QCInfo	class.ExpressionSetIllumina
QCInfo,ExpressionSetIllumina-method	class.ExpressionSetIllumina
rankInvariantNormalise	rankInvariantNormalise
rbind.BeadLevelList	cbind
read.pgmfile	readBeadLevelData
readBeadLevelData	readBeadLevelData
readBeadSummaryData	readBeadSummaryData
readBeadSummaryTargets	readBeadSummaryTargets
readBeadTargets	readBeadTargets
readCols	readBeadSummaryData
readQC	readQC
SAMSummary	interactivePlots
se.exprs,ExpressionSetIllumina-method	class.ExpressionSetIllumina
se.exprs<-,ExpressionSetIllumina,matrix-method	class.ExpressionSetIllumina
sharpen	readBeadLevelData
show, BeadLevelList-method	class-BeadLevelList
show,ExpressionSetIllumina-method	class.ExpressionSetIllumina
show,LargeDataObject-method	LargeDataObject
showTIFF	displayTIFFImage
singleQCPlot	readQC
[,ExpressionSetIllumina-method	class.ExpressionSetIllumina
[.BeadLevelList	class-BeadLevelList
