arrayNames	arrayNames
arrayNames,BeadLevelList-method	class-BeadLevelList
averagePixels	readBeadLevelData
backgroundCorrect	backgroundCorrect
backgroundCorrect,BeadLevelList,character,double,logical-method	class-BeadLevelList
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-BeadLevelList
BeadLevelList-class	class-BeadLevelList
BeadLevelNormalise	BeadLevelNormalise
BLData	BLData
boxplotBeads	boxplotBeads
BSData	BSData
calculateBackground	readBeadLevelData
calculateForegroundIntensities	readBeadLevelData
class:ExpressionSetIllumina	class.ExpressionSetIllumina
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
createBeadSummaryData, BeadLevelList-method	findBeadStatus
createBeadSummaryData,BeadLevelList-method	createBeadSummaryData
Detection	class.ExpressionSetIllumina
Detection,ExpressionSetIllumina-method	class.ExpressionSetIllumina
DiffScore	DiffScore
dim,BeadLevelList-method	class-BeadLevelList
displayTIFFImage	displayTIFFImage
ExpressionSetIllumina-class	class.ExpressionSetIllumina
exprs,ExpressionSetIllumina-method	class.ExpressionSetIllumina
exprs<-,ExpressionSetIllumina,ANY-method	class.ExpressionSetIllumina
exprs<-,ExpressionSetIllumina,matrix-method	class.ExpressionSetIllumina
findAllOutliers	findAllOutliers
findAllOutliers, BeadLevelList-method	findBeadStatus
findAllOutliers-methods	findAllOutliers
findBeadStatus	findBeadStatus
FindIlluminaSpotl	displayTIFFImage
getArrayData	getArrayData
getArrayData,BeadLevelList-method	class-BeadLevelList
getProbeIndices	findBeadStatus
getProbeIndicesC	findBeadStatus
getProbeIntensities	findBeadStatus
getProbeIntensities,BeadLevelList-method	findBeadStatus
IdentifyBeads	displayTIFFImage
IdentifyIntensity	displayTIFFImage
imageplot	imageplot
initialize,BeadLevelList-method	class-BeadLevelList
initialize,ExpressionSetIllumina-method	class.ExpressionSetIllumina
LargeDataObject-class	LargeDataObject
medianNormalise	medianNormalise
NoBeads	class.ExpressionSetIllumina
NoBeads,ExpressionSetIllumina-method	class.ExpressionSetIllumina
numBeads	numBeads
numBeads,BeadLevelList-method	class-BeadLevelList
pData,BeadLevelList-method	class-BeadLevelList
phenoData,BeadLevelList-method	class-BeadLevelList
plotBeadDensities	plotBeadDensities
plotBeadIntensities	plotBeadIntensities
plotBeadLocations	plotBeadLocations
plotMA	plotMA
plotMAXY	plotMAXY
plotOnSAM	plotOnSAM
plotRG	plotRG
plotXY	plotXY
QC	QC
qcBeadLevel	qcBeadLevel
QCInfo	class.ExpressionSetIllumina
QCInfo,ExpressionSetIllumina-method	class.ExpressionSetIllumina
rankInvariantNormalise	rankInvariantNormalise
read.pgmfile	readBeadLevelData
readBeadLevelData	readBeadLevelData
readBeadSummaryData	readBeadSummaryData
readBeadSummaryTargets	readBeadSummaryTargets
readBeadTargets	readBeadTargets
readIllumina	readIllumina
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
[,ExpressionSetIllumina-method	class.ExpressionSetIllumina
[[,BeadLevelList,ANY,missing-method	class-BeadLevelList
