$.AffyBatch	AffyBatch-class
.setAffyOptions	.setAffyOptions
affy-options	affy-options
affy.scalevalue.exprSet	affy.scalevalue.exprSet
AffyBatch	AffyBatch-class
AffyBatch-class	AffyBatch-class
affybatch.example	affybatch.example
AffyRNAdeg	AffyRNAdeg
AllButCelsForReadAffy	read.affybatch
avdiff	summary
barplot,ProbeSet-method	ProbeSet-class
barplot.ProbeSet	barplot.ProbeSet
bg.adjust	bg.adjust
bg.correct	bgc
bg.correct,AffyBatch,character-method	AffyBatch-class
bg.correct-methods	bgc
bg.correct.mas	bgc
bg.correct.methods	bgc
bg.correct.none	bgc
bg.correct.rma	bgc
bg.correct.rma2	bgc
bg.parameters	bg.adjust
bgcorrect.methods	bgc
boxplot,AffyBatch-method	AffyBatch-class
cdfenv.example	cdfenv.example
cdfFromBioC	cdfFromBioC
cdfFromData	cdfFromBioC
cdfFromEnvironment	cdfFromBioC
cdfFromLibPath	cdfFromBioC
cdfName	AffyBatch-class
cdfName,AffyBatch-method	AffyBatch-class
cleancdfname	cleancdfname
close,ProgressBarText-method	ProgressBarText-class
colnames,ProbeSet-method	ProbeSet-class
computeExprSet	generateExprSet-methods
computeExprSet,AffyBatch,character,character-method	AffyBatch-class
concentrations	SpikeIn
debug.affy123	debug.affy123
express.summary.stat	generateExprVal-methods
express.summary.stat,ProbeSet,character,character-method	ProbeSet-class
express.summary.stat-methods	generateExprVal-methods
express.summary.stat.methods	generateExprVal-methods
expresso	expresso
expressoWidget	expressoWidget
fit.li.wong	fit.li.wong
geneNames	AffyBatch-class
geneNames,AffyBatch-method	AffyBatch-class
geneNames<-	AffyBatch-class
geneNames<-,AffyBatch-method	AffyBatch-class
generateExprSet-methods	generateExprSet-methods
generateExprSet.methods	generateExprSet-methods
generateExprVal	generateExprVal-methods
generateExprVal-methods	generateExprVal-methods
generateExprVal.method.avgdiff	generateExprVal.method.avgdiff
generateExprVal.method.liwong	generateExprVal.method.avgdiff
generateExprVal.method.mas	generateExprVal.method.avgdiff
generateExprVal.method.medianpolish	generateExprVal.method.avgdiff
generateExprVal.method.playerout	generateExprVal.method.playerout
generateExprVal.methods	generateExprVal-methods
getCdfInfo	AffyBatch-class
getCdfInfo,AffyBatch-method	AffyBatch-class
hist,AffyBatch-method	AffyBatch-class
hlog	hlog
image	AffyBatch-class
image,AffyBatch-method	AffyBatch-class
indexProbes	AffyBatch-class
indexProbes,AffyBatch,character-method	AffyBatch-class
indexProbes,AffyBatch-method	AffyBatch-class
indices2xy	xy2indices
initialize,ProgressBarText-method	ProgressBarText-class
intensity	AffyBatch-class
intensity,AffyBatch-method	AffyBatch-class
intensity<-	AffyBatch-class
intensity<-,AffyBatch-method	AffyBatch-class
just.rma	justrma
justRMA	justrma
length,AffyBatch-method	AffyBatch-class
li.wong	fit.li.wong
list.celfiles	list.celfiles
loess.normalize	loess.normalize
ma.plot	MAplot
maffy.normalize	maffy.normalise
maffy.subset	maffy.subset
mapCdfName	cleancdfname
MAplot	MAplot
MAplot,AffyBatch-method	MAplot
mas5	mas5
mas5.detection	mas5calls
mas5calls	mas5calls
mas5calls,AffyBatch-method	mas5calls
mas5calls,ProbeSet-method	mas5calls
mas5calls.AffyBatch	mas5calls
mas5calls.ProbeSet	mas5calls
Mbox	MAplot
Mbox,AffyBatch-method	MAplot
medianpolish	summary
merge.AffyBatch	merge.AffyBatch
mm	probeMatch-methods
mm,AffyBatch-method	AffyBatch-class
mm,ProbeSet-method	ProbeSet-class
mm<-	probeMatch-methods
mm<-,AffyBatch,ANY-method	AffyBatch-class
mm<-,ProbeSet,matrix-method	ProbeSet-class
mmindex	AffyBatch-class
mmindex,AffyBatch-method	AffyBatch-class
multiloess	multiloess
mva.pairs	mva.pairs
ncol,AffyBatch-method	AffyBatch-class
normalize	normalize
normalize,AffyBatch-method	normalize-methods
normalize.AffyBatch	normalize-methods
normalize.AffyBatch.constant	normalize.constant
normalize.AffyBatch.contrasts	normalize.contrast
normalize.AffyBatch.invariantset	normalize.invariantset
normalize.AffyBatch.loess	normalize.loess
normalize.AffyBatch.methods	normalize-methods
normalize.AffyBatch.qspline	normalize.qspline
normalize.AffyBatch.quantiles	normalize.quantiles
normalize.AffyBatch.quantiles.robust	normalize.quantiles.robust
normalize.constant	normalize.constant
normalize.contrast	maffy.normalise
normalize.contrasts	normalize.contrast
normalize.invariantset	normalize.invariantset
normalize.loess	normalize.loess
normalize.methods	normalize-methods
normalize.methods,AffyBatch-method	normalize-methods
normalize.qspline	normalize.qspline
normalize.quantiles	normalize.quantiles
normalize.quantiles.robust	normalize.quantiles.robust
nrow,AffyBatch-method	AffyBatch-class
open,ProgressBarText-method	ProgressBarText-class
pairs.AffyBatch	pairs.AffyBatch
playerout.costfunction	generateExprVal.method.playerout
plot.ProbeSet	plot.ProbeSet
plotAffyRNAdeg	AffyRNAdeg
plotDensity	plot.density
plotDensity.AffyBatch	plot.density
plotLocation	plotLocation
pm	probeMatch-methods
pm,AffyBatch-method	AffyBatch-class
pm,ProbeSet-method	ProbeSet-class
pm<-	probeMatch-methods
pm<-,AffyBatch,ANY-method	AffyBatch-class
pm<-,ProbeSet,matrix-method	ProbeSet-class
pmcorrect	pmcorrect
pmcorrect.mas	pmcorrect
pmcorrect.methods	pmcorrect
pmcorrect.pmonly	pmcorrect
pmcorrect.subtractmm	pmcorrect
pmindex	AffyBatch-class
pmindex,AffyBatch-method	AffyBatch-class
ppset.ttest	ppsetApply
ppsetApply	ppsetApply
probeMatch	probeMatch-methods
probeMatch-methods	probeMatch-methods
probeNames	probeNames-methods
probeNames,AffyBatch-method	AffyBatch-class
probeNames-methods	probeNames-methods
probeNames<-	probeNames-methods
probes	AffyBatch-class
probes,AffyBatch-method	AffyBatch-class
probeset	AffyBatch-class
probeset,AffyBatch-method	AffyBatch-class
ProbeSet-class	ProbeSet-class
ProgressBarText-class	ProgressBarText-class
qspline-normalize	normalize.qspline
read.affybatch	read.affybatch
read.probematrix	read.probematrix
ReadAffy	read.affybatch
rma	rma
sampleNames,ProbeSet-method	ProbeSet-class
show,AffyBatch-method	AffyBatch-class
show,ProbeSet-method	ProbeSet-class
simplemultiLoess	simplemultiLoess
SpikeIn	SpikeIn
summary	summary
summaryAffyRNAdeg	AffyRNAdeg
tukey.biweight	tukey.biweight
tukeybiweight	summary
update,ProgressBarText-method	ProgressBarText-class
whatcdf	whatcdf
xy2indices	xy2indices
[,AffyBatch-method	AffyBatch-class
[<-,AffyBatch-method	AffyBatch-class
[[,AffyBatch-method	AffyBatch-class
