all.present	all.present
all.present.in.group	all.present.in.group
arrayType	QCStats-class
arrayType,QCStats-method	QCStats-class
arrayType-method	QCStats-class
avbg	QCStats-class
avbg,QCStats-method	QCStats-class
avbg-method	QCStats-class
bg.correct.sa	bg.correct.sa
blue.white.red.cols	hmap.colors
calculated.from	PairComp-class
calculated.from,PairComp-method	PairComp-class
call.exprs	call.exprs
calls	PairComp-class
calls,PairComp-method	PairComp-class
detection.p.val	detection.p.val
fc	PairComp-class
fc,PairComp-method	PairComp-class
get.annotation	get.annotation
get.array.indices	get.array.indices
get.array.indices,AffyBatch-method	get.array.indices
get.array.indices,exprSet-method	get.array.indices
get.array.subset	get.array.subset
get.array.subset,AffyBatch-method	get.array.subset
get.array.subset,ExpressionSet-method	get.array.subset
get.array.subset.affybatch	get.array.subset.affy
get.array.subset.exprset	get.array.subset.affy
get.fold.change.and.t.test	get.fold.change.and.t.test
getActin3	simpleaffy-deprecated
getActin5	simpleaffy-deprecated
getActinM	simpleaffy-deprecated
getAllQCProbes	simpleaffy-deprecated
getAllSpikeProbes	simpleaffy-deprecated
getAlpha1	simpleaffy-deprecated
getAlpha2	simpleaffy-deprecated
getBioB	simpleaffy-deprecated
getBioC	simpleaffy-deprecated
getBioD	simpleaffy-deprecated
getCreX	simpleaffy-deprecated
getGapdh3	simpleaffy-deprecated
getGapdh5	simpleaffy-deprecated
getGapdhM	simpleaffy-deprecated
getTao	simpleaffy-deprecated
group	PairComp-class
group,PairComp-method	PairComp-class
haveQCParams	simpleaffy-deprecated
hmap.eset	hmap.eset
hmap.pc	hmap.pc
journalpng	journalpng
justMAS	justMAS
maxbg	QCStats-class
maxbg,QCStats-method	QCStats-class
maxbg-method	QCStats-class
means	PairComp-class
means,PairComp-method	PairComp-class
members	PairComp-class
members,PairComp-method	PairComp-class
minbg	QCStats-class
minbg,QCStats-method	QCStats-class
minbg-method	QCStats-class
PairComp-class	PairComp-class
pairwise.comparison	pairwise.comparison
pairwise.filter	pairwise.filter
pairwise.filter,PairComp-method	PairComp-class
pData	PairComp-class
pData,PairComp-method	PairComp-class
percent.present	QCStats-class
percent.present,QCStats-method	QCStats-class
percent.present-method	QCStats-class
plot,PairComp	plot.pairwise.comparison
plot,PairComp,ANY-method	PairComp-class
plot,PairComp-method	plot.pairwise.comparison
plot,QCStats	plot.qc.stats
plot,QCStats,ANY-method	QCStats-class
plot,QCStats,missing-method	plot.qc.stats
plot.pairwise.comparison	plot.pairwise.comparison
plot.qc.stats	plot.qc.stats
qc	qc
qc,AffyBatch-method	qc
qc.add.probe	qc.get.probes
qc.add.ratio	qc.get.ratios
qc.add.spike	qc.get.spikes
qc.affy	qc.affy
qc.get.alpha1	qc.get.alpha1
qc.get.alpha2	qc.get.alpha1
qc.get.array	qc.get.array
qc.get.probe	qc.get.probes
qc.get.probes	qc.get.probes
qc.get.ratio	qc.get.ratios
qc.get.ratios	qc.get.ratios
qc.get.spike	qc.get.spikes
qc.get.spikes	qc.get.spikes
qc.get.tau	qc.get.alpha1
qc.have.params	qc.have.params
qc.ok	qc.ok
qc.read.file	qc.read.file
qc.set.alpha1	qc.get.alpha1
qc.set.alpha2	qc.get.alpha1
qc.set.array	qc.get.array
qcProbes	QCStats-class
qcProbes,QCStats-method	QCStats-class
qcProbes-method	QCStats-class
qcs	qc.stats
QCStats-class	QCStats-class
ratios	QCStats-class
ratios,QCStats-method	QCStats-class
ratios-method	QCStats-class
read.affy	read.affy
read.affy.mixed	read.affy.mixed
red.black.green.cols	hmap.colors
red.yellow.white.cols	hmap.colors
results.summary	get.annotation
screenpng	journalpng
setQCEnvironment	setQCEnvironment
sfs	QCStats-class
sfs,QCStats-method	QCStats-class
sfs-method	QCStats-class
simpleaffy-deprecated	simpleaffy-deprecated
spikeInProbes	QCStats-class
spikeInProbes,QCStats-method	QCStats-class
spikeInProbes-method	QCStats-class
standard.pearson	standard.pearson
target	QCStats-class
target,QCStats-method	QCStats-class
target-method	QCStats-class
trad.scatter.plot	trad.scatter.plot
tt	PairComp-class
tt,PairComp-method	PairComp-class
write.annotation	get.annotation
[,PairComp-method	PairComp-class
[<-,PairComp-method	PairComp-class