1.Introduction	1introduction
2.Classes	2classes
3.ReadingData	3reading
4.Normalization	4normalization
5.LinearModels	5linearmodels
6.Diagnostics	6diagnostics
a.spot	m.spot
anova.MAList	anova-method
as.MAList	asmalist
backgroundCorrect	backgroundcorrect
bwss	bwss
bwss.matrix	bwss.matrix
cbind.MAList	cbind
cbind.RGList	cbind
classifyTests	classifytests
classifyTestsP	classifytests
classifyTestsT	classifytests
contrasts.fit	contrasts.fit
controlStatus	controlStatus
designMatrix	designMatrix
dim.MAList	dim
dim.MArrayLM	dim
dim.RGList	dim
dupcor.series	dupcor
duplicateCorrelation	dupcor
eBayes	ebayes
ebayes	ebayes
exprSet2-class	exprset2
fitFDist	fitfdist
getLayout	getlayout
gls.series	gls.series
gridc	gridspotrc
gridr	gridspotrc
heatDiagram	heatdiagram
heatdiagram	heatdiagram
helpMethods	helpMethods
imageplot	imageplot
is.fullrank	isfullrank
isNumeric	isnumeric
kooperberg	kooperberg
LargeDataObject-class	LargeDataObject
lm.series	lm.series
lmFit	lmFit
loessFit	loessfit
m.spot	m.spot
MA.RG	normalizeWithinArrays
makeContrasts	makeContrasts
makeUnique	makeunique
MAList-class	malist
MArrayLM-class	marraylm
matvec	matvec
merge.RGList	merge
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
printHead	printHead
PrintLayout-class	PrintLayout
printorder	printorder
qqt	qqt
QualityWeights	qualwt
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
splitName	splitName
spotc	gridspotrc
spotr	gridspotrc
tmixture.matrix	tmixture
tmixture.vector	tmixture
topTable	toptable
toptable	toptable
trigammaInverse	trigammainverse
uniquegenelist	uniquegenelist
unwrapdups	unwrapdups
vecmat	matvec
vennCounts	venn
vennDiagram	venn
wtarea	qualwt
wtflags	qualwt
wtIgnore.Filter	qualwt
zscoreGamma	zscore
zscoreT	zscore
[.MAList	subsetting
[.RGList	subsetting
