1.Introduction	1introduction
2.Classes	2classes
3.ReadingData	3reading
4.Normalization	4normalization
5.LinearModels	5linearmodels
6.SingleChannel	6SingleChannel
7.Diagnostics	7diagnostics
8.Other	8Other
a.spot	m.spot
anova.MAList	anova-method
array2channel	array2channel
as.MAList	asmalist
auROC	auROC
backgroundCorrect	backgroundcorrect
blockDiag	blockDiag
bwss	bwss
bwss.matrix	bwss.matrix
cbind.MAList	cbind
cbind.RGList	cbind
classifyTests	classifytests-deprecated
classifyTestsF	classifytests
classifyTestsP	classifytests
classifyTestsT	classifytests
coerce,RGList,exprSet2-method	rglist
contrasts.fit	contrasts.fit
controlStatus	controlStatus
designMatrix	designMatrix-deprecated
dim.MAList	dim
dim.MArrayLM	dim
dim.RGList	dim
dimnames.MAList	dimnames
dimnames.MArrayLM	dimnames
dimnames.RGList	dimnames
dupcor.series	dupcor
duplicateCorrelation	dupcor
eBayes	ebayes
ebayes	ebayes
exprSet2-class	exprset2
fitFDist	fitfdist
FStat	classifytests
getLayout	getlayout
getSpacing	getSpacing
gls.series	gls.series
gridc	gridspotrc
gridr	gridspotrc
heatDiagram	heatdiagram
heatdiagram	heatdiagram
helpMethods	helpMethods
imageplot	imageplot
intraspotCorrelation	intraspotCorrelation
is.fullrank	isfullrank
isNumeric	isnumeric
kooperberg	kooperberg
LargeDataObject-class	LargeDataObject
length.MAList	dim
length.MArrayLM	dim
length.RGList	dim
limmaguideURL	limmaguideURL
lm.series	lm.series
lmFit	lmFit
lmscFit	lmscFit
loessFit	loessfit
m.spot	m.spot
MA.RG	normalizeWithinArrays
ma3x3.matrix	ma3x3
ma3x3.spottedarray	ma3x3
makeContrasts	makeContrasts
makeUnique	makeunique
MAList-class	malist
MArrayLM-class	marraylm
matvec	matvec
merge.MAList	merge
merge.RGList	merge
modelMatrix	modelMatrix
modifyWeights	modifyWeights
normalizeBetweenArrays	normalizebetweenarrays
normalizeForPrintorder	normalizeprintorder
normalizeForPrintorder.rg	normalizeprintorder
normalizeMedianDeviations	normalizescale
normalizeMedians	normalizescale
normalizeQuantiles	normalizequantiles
normalizeRobustSpline	normalizeRobustSpline
normalizeWithinArrays	normalizeWithinArrays
plotDensities	plotDensities
plotMA	plotma
plotPrintorder	normalizeprintorder
plotPrintTipLoess	plotprinttiploess
poolVar	poolvar
printHead	printHead
PrintLayout-class	PrintLayout
printorder	printorder
qqt	qqt
QualityWeights	qualwt
rbind.MAList	cbind
rbind.RGList	cbind
read.imagene	read.maimages
read.maimages	read.maimages
read.matrix	read.matrix
read.series	read.series
readGAL	readgal
readGPRHeaders	readGPRHeaders
readImageneHeaders	readImageneHeaders
readSpotTypes	readSpotTypes
readTargets	readTargets
removeExt	removeext
rg.genepix	rg.genepix
RG.MA	normalizeWithinArrays
rg.quantarray	rg.quantarray
rg.series.spot	rg.series.spot
rg.spot	rg.spot
RGList-class	rglist
rlm.series	rlm.series
show,LargeDataObject-method	LargeDataObject
show,TestResults-method	TestResults
splitName	splitName
spotc	gridspotrc
spotr	gridspotrc
squeezeVar	squeezeVar
summary.TestResults	TestResults
TestResults-class	TestResults
tmixture.matrix	tmixture
tmixture.vector	tmixture
topTable	toptable
toptable	toptable
trigammaInverse	trigammainverse
uniquegenelist	uniquegenelist
uniqueTargets	modelMatrix
unwrapdups	unwrapdups
vecmat	matvec
vennCounts	venn
vennDiagram	venn
write.fit	writefit
wtarea	qualwt
wtflags	qualwt
wtIgnore.Filter	qualwt
zscoreGamma	zscore
zscoreT	zscore
[.MAList	subsetting
[.RGList	subsetting
