addArrayMask	addArrayMask
arrayNames	arrayNames
arrayNames,BeadLevelList-method	class-BeadLevelList
backgroundControlPlot	backgroundControlPlot
backgroundCorrect	backgroundCorrect
backgroundCorrect,BeadLevelList,character,double,logical-method	class-BeadLevelList
backgroundCorrect,BeadLevelList-method	backgroundCorrect
backgroundCorrect,RGList-method	backgroundCorrect
BASH	BASH
BASHCompact	BASHCompact
BASHDiffuse	BASHDiffuse
BASHExtended	BASHExtended
beadarrayUsersGuide	beadarrayUsersGuide
BeadChipSummary	interactivePlots
BeadLevelList	class-BeadLevelList
BeadLevelList-class	class-BeadLevelList
beadResids	beadResids
BGFilter	BGFilter
BGFilterWeighted	BGFilterWeighted
BLData	BLData
boxplotBeads	boxplotBeads
BSData	BSData
calculateBeadLevelScores	calculateBeadLevelScores
calculateDetection	calculateDetection
chooseClusters	chooseClusters
class:ExpressionSetIllumina	class.ExpressionSetIllumina
clearArrayMask	addArrayMask
closeImage	closeImage
combine,ExpressionSetIllumina,ANY-method	class.ExpressionSetIllumina
combine,ExpressionSetIllumina,ExpressionSetIllumina-method	class.ExpressionSetIllumina
combineBeadLevelLists	combineBeadLevelLists
combineBeadLevelLists,BeadLevelList-method	class-BeadLevelList
copyBeadLevelList	copyBeadLevelLists
copyBeadLevelList,BeadLevelList-method	class-BeadLevelList
createBeadSummaryData	createBeadSummaryData
denseRegions	denseRegions
Detection	class.ExpressionSetIllumina
Detection,ExpressionSetIllumina-method	class.ExpressionSetIllumina
Detection<-	class.ExpressionSetIllumina
Detection<-,ExpressionSetIllumina,matrix-method	class.ExpressionSetIllumina
dim,BeadLevelList-method	class-BeadLevelList
ExpressionControlData	ExpressionControlData
ExpressionSetIllumina-class	class.ExpressionSetIllumina
exprs,ExpressionSetIllumina-method	class.ExpressionSetIllumina
exprs<-,ExpressionSetIllumina,matrix-method	class.ExpressionSetIllumina
findAllOutliers	findAllOutliers
findBeadStatus	findBeadStatus
generateE	generateE
generateNeighbours	generateNeighbours
getAnnotation	getAnnotation
getArrayData	getArrayData
getArrayData,BeadLevelList-method	class-BeadLevelList
getControlAnno	getAnnotation
getProbeIntensities	findBeadStatus
getProbeIntensities,BeadLevelList-method	findBeadStatus
getVariance	getVariance
getVariance,ExpressionSetIllumina-method	class.ExpressionSetIllumina
gradientPlot	calculateBeadLevelScores
HULK	HULK
HULKResids	HULKResids
imageplot	imageplot
initialize,BeadLevelList-method	class-BeadLevelList
initialize,ExpressionSetIllumina-method	class.ExpressionSetIllumina
lmhPlot	lmhPlot
medianNormalise	medianNormalise
NoBeads	class.ExpressionSetIllumina
NoBeads,ExpressionSetIllumina-method	class.ExpressionSetIllumina
NoBeads<-	class.ExpressionSetIllumina
NoBeads<-,ExpressionSetIllumina,matrix-method	class.ExpressionSetIllumina
normaliseIllumina	normaliseIllumina
numBeads	numBeads
numBeads,BeadLevelList-method	class-BeadLevelList
outlierPlot	outlierplot
pData,BeadLevelList-method	class-BeadLevelList
phenoData,BeadLevelList-method	class-BeadLevelList
plotBeadDensities	plotBeadDensities
plotBeadIntensities	plotBeadIntensities
plotBeadLocations	plotBeadLocations
plotMA	plotMA
plotMAXY	plotMAXY
plotOnSAM	plotOnSAM
plotRG	plotRG
plotTIFF	plotTIFF
plotXY	plotXY
poscontPlot	poscontPlot
probePairsPlot	probePairsPlot
qcBeadLevel	qcBeadLevel
QCInfo	class.ExpressionSetIllumina
QCInfo,ExpressionSetIllumina-method	class.ExpressionSetIllumina
QCInfo<-	class.ExpressionSetIllumina
QCInfo<-,ExpressionSetIllumina,list-method	class.ExpressionSetIllumina
rankInvariantNormalise	rankInvariantNormalise
readBeadSummaryData	readBeadSummaryData
readBGX	readBGX
readIllumina	readIllumina
readLocs	readLocs
readQC	readQC
readTIFF	readTIFF
removeArrayMask	addArrayMask
SAMSummary	interactivePlots
se.exprs,ExpressionSetIllumina-method	class.ExpressionSetIllumina
se.exprs<-,ExpressionSetIllumina,matrix-method	class.ExpressionSetIllumina
setAnnotation	getAnnotation
setWeights	setWeights
show,BeadLevelList-method	class-BeadLevelList
show,ExpressionSetIllumina-method	class.ExpressionSetIllumina
showArrayMask	addArrayMask
viewBeads	viewBeads
[,ExpressionSetIllumina-method	class.ExpressionSetIllumina
[[,BeadLevelList,ANY,missing-method	class-BeadLevelList
