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 |
| .onAttach | 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 |
