API for simpleaffy
Very simple high level analysis of Affymetrix data

Global functions
.bg.stats Source code
.createEmptyQCEnvironment Source code
.get.array.def.file Source code
.getRatios Source code
.if.probeset.not.found Source code
.initializeQCEnvironment Source code
.maplot Source code
.mas5 Source code
.pcscatterplot Source code
.qc.file.addQCRatio Source code
.qc.file.addQCSpike Source code
.qc.file.setAlpha1 Source code
.qc.file.setAlpha2 Source code
.qc.file.setQCArray Source code
.qc.is.empty Source code
.qc.set.empty Source code
.qc.test Source code
.strip.list Source code
.volcanoplot Source code
PairComp-class Man page
QCStats-class Man page
[,PairComp-method Man page
[<-,PairComp-method Man page
all.present Man page Source code
all.present.in.group Man page Source code
arrayType Man page
arrayType,QCStats-method Man page
arrayType-method Man page
avbg Man page
avbg,QCStats-method Man page
avbg-method Man page
bg.correct.sa Man page Source code
blue.white.red.cols Man page
calculated.from Man page
calculated.from,PairComp-method Man page
call.exprs Man page
calls Man page
calls,PairComp-method Man page
detection.p.val Man page Source code
fc Man page
fc,PairComp-method Man page
get.annotation Man page
get.array.indices Man page
get.array.indices,AffyBatch-method Man page
get.array.indices,ExpressionSet-method Man page
get.array.subset Man page
get.array.subset,AffyBatch-method Man page
get.array.subset,ExpressionSet-method Man page
get.array.subset.affybatch Man page
get.array.subset.exprset Man page
get.fold.change.and.t.test Man page
getActin3 Man page Source code
getActin5 Man page Source code
getActinM Man page Source code
getAllQCProbes Man page Source code
getAllSpikeProbes Man page Source code
getAlpha1 Man page Source code
getAlpha2 Man page Source code
getBioB Man page Source code
getBioC Man page Source code
getBioD Man page Source code
getCreX Man page Source code
getGapdh3 Man page Source code
getGapdh5 Man page Source code
getGapdhM Man page Source code
getTao Man page Source code
group Man page
group,PairComp-method Man page
haveQCParams Man page Source code
hmap.eset Man page Source code
hmap.pc Man page Source code
journalpng Man page Source code
justMAS Man page Source code
maxbg Man page
maxbg,QCStats-method Man page
maxbg-method Man page
means Man page
means,PairComp-method Man page
members Man page
members,PairComp-method Man page
minbg Man page
minbg,QCStats-method Man page
minbg-method Man page
pData Man page
pData,PairComp-method Man page
pairwise.comparison Man page
pairwise.filter Man page Source code
pairwise.filter,PairComp-method Man page
percent.present Man page
percent.present,QCStats-method Man page
percent.present-method Man page
plot,PairComp Man page
plot,PairComp,ANY-method Man page
plot,PairComp,PairComp-method Man page
plot,PairComp,missing-method Man page
plot,PairComp-method Man page
plot,QCStats Man page
plot,QCStats,ANY-method Man page
plot,QCStats,missing-method Man page
plot.pairwise.comparison Man page Source code
plot.qc.stats Man page Source code
qc Man page
qc,AffyBatch-method Man page
qc.add.probe Man page Source code
qc.add.ratio Man page Source code
qc.add.spike Man page Source code
qc.affy Man page Source code
qc.get.alpha1 Man page Source code
qc.get.alpha2 Man page Source code
qc.get.array Man page Source code
qc.get.probe Man page Source code
qc.get.probes Man page Source code
qc.get.ratio Man page Source code
qc.get.ratios Man page Source code
qc.get.spike Man page Source code
qc.get.spikes Man page Source code
qc.get.tau Man page Source code
qc.have.params Man page Source code
qc.ok Man page Source code
qc.read.file Man page Source code
qc.set.alpha1 Man page Source code
qc.set.alpha2 Man page Source code
qc.set.array Man page Source code
qcProbes Man page
qcProbes,QCStats-method Man page
qcProbes-method Man page
qcs Man page
ratios Man page
ratios,QCStats-method Man page
ratios-method Man page
read.affy Man page Source code
read.affy.mixed Man page
red.black.green.cols Man page
red.yellow.white.cols Man page
results.summary Man page Source code
screenpng Man page Source code
setQCEnvironment Man page Source code
sfs Man page
sfs,QCStats-method Man page
sfs-method Man page
simpleaffy-deprecated Man page
spikeInProbes Man page
spikeInProbes,QCStats-method Man page
spikeInProbes-method Man page
standard.pearson Man page Source code
target Man page
target,QCStats-method Man page
target-method Man page
trad.scatter.plot Man page
tt Man page
tt,PairComp-method Man page
write.annotation Man page Source code
simpleaffy documentation built on April 29, 2020, 3:37 a.m.