averagePixels	readBeadImages
backgroundCorrectBeads	backgroundCorrectBeads
BeadLevelList-class	BeadLevelList
BeadSummaryList-class	BeadSummaryList
biotin_controls	biotin_controls
BLData	BLData
BSData	BSData
calculateBackground	readBeadImages
calculateForegroundIntensities	readBeadImages
cbind.BeadLevelList	cbind
cbind.BeadSummaryList	cbind
checkRandomness	checkRandomness
chitest	checkRandomness
coerce,BeadLevelList,exprSet2-method	BeadLevelList
createBeadSummaryData	createBeadSummaryData
cy3_controls	cy3_controls
dim.BeadLevelList	dim
dim.BeadSummaryList	dim
dimnames.BeadLevelList	dimnames
dimnames.BeadSummaryList	dimnames
displayTIFFImage	displayTIFFImage
findAllOutliers	findAllOutliers
findBeadStatus	findBeadStatus
findHighestChis	findHighestChis
findHighestSD	findHighestSD
FindIlluminaSpotl	displayTIFFImage
findLowestCounts	findLowestCounts
findMostOutliers	findMostOutliers
getDimensions	getDimensions
getMeanIntensities	getMeanIntensities
getProbeCoords	getProbeCoords
getProbeIDs	getProbeIDs
getProbeIndices	findBeadStatus
getProbeIndicesC	findBeadStatus
getProbeInfo	getProbeInfo
getProbeIntensities	getProbeIntensities
getUnregisteredBeads	getUnregisteredBeads
histBeadCounts	histBeadCounts
housekeeping_controls	housekeeping_controls
hs_controls	hs_controls
IdentifyBeads	displayTIFFImage
IdentifyIntensity	displayTIFFImage
labelling_controls	labelling_controls
LargeDataObject-class	LargeDataObject
length.BeadLevelList	dim
length.BeadSummaryList	dim
ls_controls	ls_controls
matrix.mean	matrix.mean
medianNormalise	medianNormalise
neg_controls	neg_controls
normalizeBetweenArrays	quantileNormalise
other_controls	other_controls
pairwiseMA	pairwiseMA
panel.MA	pairwiseMA
panel.XY	pairwiseMA
plotArray	plotArray
plotBeadIntensities	plotBeadIntensities
plotBeadLocations	plotBeadLocations
plotCluster	plotCluster
plotCoords	plotBeadLocations
plotDistances	plotDistances
plotMA.beads	plotMA.beads
plotMAXY	plotMAXY
plotOnSAM	plotOnSAM
plotProbeDistances	plotProbeDistances
plotProbeVariation	plotProbeVariation
plotXY.beads	plotXY.beads
printHead	subsetting
probeCluster	plotCluster
probeDiagnostics	probeDiagnostics
qsplineNormalise	qsplineNormalise
quantileNormalise	quantileNormalise
rbind.BeadSummaryList	cbind
read.pgmfile	readBeadImages
readBeadImages	readBeadImages
readBeadSummaryData	readBeadSummaryData
readBeadSummaryTargets	readBeadSummaryTargets
readBeadTargets	readBeadTargets
readCols	readBeadSummaryData
readNonXYData	readNonXYData
readProbeInfo	readProbeInfo
Recenter	displayTIFFImage
removeArrays	removeArrays
sharpen	readBeadImages
show,LargeDataObject-method	LargeDataObject
showTIFF	displayTIFFImage
[.BeadLevelList	subsetting
[.BeadSummaryList	subsetting
