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	targetsA2C
arrayWeights	arrayWeights
arrayWeightsQuick	arrayWeightsQuick
as.data.frame.MArrayLM	asdataframe
as.MAList	asmalist
as.matrix.exprSet	asmatrix
as.matrix.MAList	asmatrix
as.matrix.MArrayLM	asmatrix
as.matrix.marrayNorm	asmatrix
as.matrix.RGList	asmatrix
auROC	auROC
backgroundCorrect	backgroundcorrect
blockDiag	blockDiag
bwss	bwss
bwss.matrix	bwss.matrix
cbind.MAList	cbind
cbind.RGList	cbind
changeLog	changelog
classifyTests	classifytests-deprecated
classifyTestsF	classifytests
classifyTestsP	classifytests
classifyTestsT	classifytests
coerce,RGList,exprSet2-method	rglist
contrasts.fit	contrasts.fit
controlStatus	controlStatus
convest	convest
decideTests	decideTests
designI2A	channel2M
designI2M	channel2M
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
fit.normexp	fitnormexp
fit.normexp0	fitnormexp
fitFDist	fitfdist
FStat	classifytests
geneSetTest	geneSetTest
getLayout	getlayout
getLayout2	getlayout
getSpacing	getSpacing
gls.series	gls.series
gridc	gridspotrc
gridr	gridspotrc
grloglik	m2logliknormexp
grsumloglik	m2logliknormexp
heatDiagram	heatdiagram
heatdiagram	heatdiagram
helpMethods	helpMethods
imageplot	imageplot
imageplot3by2	imageplot3by2
intraspotCorrelation	intraspotCorrelation
is.fullrank	isfullrank
isNumeric	isnumeric
kooperberg	kooperberg
LargeDataObject-class	LargeDataObject
length.MAList	dim
length.MArrayLM	dim
length.RGList	dim
limmaUsersGuide	limmaUsersGuide
lm.series	lm.series
lmFit	lmFit
lmscFit	lmscFit
loessFit	loessfit
m.spot	m.spot
m2loglik.normexp	m2logliknormexp
MA.RG	normalizeWithinArrays
ma3x3.matrix	ma3x3
ma3x3.spottedarray	ma3x3
makeContrasts	makeContrasts
makeUnique	makeunique
MAList-class	malist
MArrayLM-class	marraylm
matvec	matvec
mdplot	mdplot
merge.MAList	merge
merge.RGList	merge
modelMatrix	modelMatrix
modifyWeights	modifyWeights
mrlm	rlm.series
nonEstimable	isfullrank
normalizeBetweenArrays	normalizebetweenarrays
normalizeForPrintorder	normalizeprintorder
normalizeForPrintorder.rg	normalizeprintorder
normalizeMedianDeviations	normalizescale
normalizeMedians	normalizescale
normalizeQuantiles	normalizequantiles
normalizeRobustSpline	normalizeRobustSpline
normalizeWithinArrays	normalizeWithinArrays
plotDensities	plotDensities
plotMA	plotma
plotMA3by2	plotma3by2
plotPrintorder	normalizeprintorder
plotPrintTipLoess	plotprinttiploess
poolVar	poolvar
printHead	printHead
PrintLayout-class	PrintLayout
printorder	printorder
protectMetachar	protectMetachar
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
readGPRHeader	readGPRHeader
readImaGeneHeader	readImaGeneHeader
readSMDHeader	readGPRHeader
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
signal.normexp	signalnormexp
splitName	splitName
spotc	gridspotrc
spotr	gridspotrc
squeezeVar	squeezeVar
sumloglik	m2logliknormexp
summary.MAList	summary
summary.MArrayLM	summary
summary.RGList	summary
summary.TestResults	TestResults
targetsA2C	targetsA2C
TestResults-class	TestResults
tmixture.matrix	tmixture
tmixture.vector	tmixture
topTable	toptable
toptable	toptable
trigammaInverse	trigammainverse
trimWhiteSpace	trimWhiteSpace
tZscore	zscore
uniquegenelist	uniquegenelist
uniqueTargets	modelMatrix
unwrapdups	unwrapdups
vecmat	matvec
vennCounts	venn
vennDiagram	venn
volcanoplot	volcanoplot
write.fit	writefit
wtarea	qualwt
wtflags	qualwt
wtIgnore.Filter	qualwt
zscoreGamma	zscore
zscoreT	zscore
[.MAList	subsetting
[.MArrayLM	subsetting
[.RGList	subsetting
