API for benilton/oligoOld
Preprocessing tools for oligonucleotide arrays

Global functions
MAplot	Man page
MAplot,ExpressionSet-method	Man page
MAplot,FeatureSet-method	Man page
MAplot,PLMset-method	Man page
MAplot,TilingFeatureSet-method	Man page
MAplot,matrix-method	Man page
MAplot-methods	Man page
NUSE	Man page
NUSE,oligoPLM-method	Man page
RLE	Man page
RLE,oligoPLM-method	Man page
annotation,oligoPLM-method	Man page
availProbeInfo	Man page
backgroundCorrect	Man page
backgroundCorrect,FeatureSet-method	Man page
backgroundCorrect,ff_matrix-method	Man page
backgroundCorrect,matrix-method	Man page
backgroundCorrect-methods	Man page
backgroundCorrectionMethods	Man page
basecontent	Man page
basicPLM	Man page
basicRMA	Man page
bg	Man page
bg,FeatureSet-method	Man page
bg,TilingFeatureSet-method	Man page
bg<-	Man page
bg<-,FeatureSet,ff_matrix-method	Man page
bg<-,FeatureSet,matrix-method	Man page
bg<-,TilingFeatureSet,array-method	Man page
bgSequence	Man page
bgSequence,DBPDInfo-method	Man page
bgSequence,ExonFeatureSet-method	Man page
bgSequence,FeatureSet-method	Man page
bgSequence,GeneFeatureSet-method	Man page
bgindex	Man page
bgindex,DBPDInfo-method	Man page
bgindex,FeatureSet-method	Man page
boxplot	Man page
boxplot,ExpressionSet-method	Man page
boxplot,FeatureSet-method	Man page
boxplot,PLMset-method	Man page
boxplot,oligoPLM-method	Man page
boxplot-methods	Man page
chromosome	Man page
chromosome<-	Man page
chromosome<-,AnnotatedDataFrame,character-method	Man page
cleanPlatformName	Man page
coef,oligoPLM-method	Man page
coefs	Man page
coefs.probe	Man page
coefs.probe,oligoPLM-method	Man page
crlmm	Man page
darkColors	Man page
divColors	Man page
fitPLM	Man page
fitProbeLevelModel	Man page
geometry,oligoPLM-method	Man page
getAffinitySplineCoefficients	Man page
getBaseProfile	Man page
getContainer	Man page
getContainer,TilingFeatureSet-method	Man page
getContainer-methods	Man page
getCrlmmSummaries	Man page
getNetAffx	Man page
getNetAffx,ExpressionSet-method	Man page
getNetAffx-methods	Man page
getNgsColorsInfo	Man page
getPD	Man page
getPlatformDesign	Man page
getPlatformDesign,FeatureSet-method	Man page
getProbeInfo	Man page
getX	Man page
getX,DBPDInfo-method	Man page
getX,FeatureSet-method	Man page
getX-methods	Man page
getY	Man page
getY,DBPDInfo-method	Man page
getY,FeatureSet-method	Man page
getY-methods	Man page
hist	Man page
hist,ExpressionSet-method	Man page
hist,FeatureSet-method	Man page
hist-methods	Man page
image	Man page
image,FeatureSet-method	Man page
image,PLMset-method	Man page
image,oligoPLM-method	Man page
image-methods	Man page
intensity	Man page
intensity,FeatureSet-method	Man page
intensity<-	Man page
intensity<-,FeatureSet-method	Man page
justCRLMM	Man page
justSNPRMA	Man page
list.xysfiles	Man page
manufacturer,oligoPLM-method	Man page
method	Man page
method,oligoPLM-method	Man page
mm	Man page
mm,FeatureSet-method	Man page
mm,TilingFeatureSet-method	Man page
mm<-	Man page
mm<-,FeatureSet,ANY,ANY,ff_matrix-method	Man page
mm<-,FeatureSet,ANY,ANY,matrix-method	Man page
mm<-,TilingFeatureSet,ANY,ANY,array-method	Man page
mmSequence	Man page
mmSequence,AffySNPPDInfo-method	Man page
mmSequence,DBPDInfo-method	Man page
mmSequence,FeatureSet-method	Man page
mmindex	Man page
mmindex,DBPDInfo-method	Man page
mmindex,FeatureSet-method	Man page
ncol,oligoPLM-method	Man page
normalizationMethods	Man page
normalize,FeatureSet-method	Man page
normalize,ff_matrix-method	Man page
normalize,matrix-method	Man page
normalizeToTarget	Man page
normalizeToTarget,ff_matrix-method	Man page
normalizeToTarget,matrix-method	Man page
normalizeToTarget-methods	Man page
nprobes	Man page
nprobes,oligoPLM-method	Man page
nprobesets	Man page
nprobesets,oligoPLM-method	Man page
oligo-defunct	Man page
oligo-package	Man page
oligoPLM	Man page
oligoPLM-class	Man page
paCalls	Man page
paCalls,ExonFeatureSet-method	Man page
paCalls,ExpressionFeatureSet-method	Man page
paCalls,GeneFeatureSet-method	Man page
plotM	Man page
plotM,SnpQSet,character-method	Man page
plotM,SnpQSet,integer-method	Man page
plotM,SnpQSet,numeric-method	Man page
plotM,TilingQSet,missing-method	Man page
plotM-methods	Man page
pm	Man page
pm,FeatureSet-method	Man page
pm,GenericFeatureSet-method	Man page
pm,TilingFeatureSet-method	Man page
pm<-	Man page
pm<-,FeatureSet,ANY,ANY,ff_matrix-method	Man page
pm<-,FeatureSet,ANY,ANY,matrix-method	Man page
pm<-,GenericFeatureSet,ANY,ANY,ff_matrix-method	Man page
pm<-,GenericFeatureSet,ANY,ANY,matrix-method	Man page
pm<-,TilingFeatureSet,ANY,ANY,array-method	Man page
pmAllele	Man page
pmAllele,AffySNPPDInfo-method	Man page
pmAllele,SnpFeatureSet-method	Man page
pmChr	Man page
pmChr,ExonFeatureSet-method	Man page
pmChr,FeatureSet-method	Man page
pmChr,GeneFeatureSet-method	Man page
pmFragmentLength	Man page
pmFragmentLength,AffySNPPDInfo-method	Man page
pmFragmentLength,SnpFeatureSet-method	Man page
pmOffset	Man page
pmOffset,AffySNPPDInfo-method	Man page
pmPosition	Man page
pmPosition,ExpressionPDInfo-method	Man page
pmPosition,FeatureSet-method	Man page
pmPosition,TilingFeatureSet-method	Man page
pmPosition,TilingPDInfo-method	Man page
pmSequence	Man page
pmSequence,AffyGenePDInfo-method	Man page
pmSequence,AffySNPPDInfo-method	Man page
pmSequence,DBPDInfo-method	Man page
pmSequence,ExonFeatureSet-method	Man page
pmSequence,FeatureSet-method	Man page
pmSequence,GeneFeatureSet-method	Man page
pmSequence,stArrayDBPDInfo-method	Man page
pmStrand	Man page
pmStrand,AffySNPPDInfo-method	Man page
pmStrand,TilingFeatureSet-method	Man page
pmindex	Man page
pmindex,DBPDInfo-method	Man page
pmindex,FeatureSet-method	Man page
pmindex,GenericFeatureSet-method	Man page
pmindex,GenericPDInfo-method	Man page
pmindex,stArrayDBPDInfo-method	Man page
probeNames	Man page
probeNames,DBPDInfo-method	Man page
probeNames,ExonFeatureSet-method	Man page
probeNames,FeatureSet-method	Man page
probeNames,GeneFeatureSet-method	Man page
probeNames,stArrayDBPDInfo-method	Man page
probesetNames	Man page
probesetNames,FeatureSet-method	Man page
read.celfiles	Man page
read.celfiles2	Man page
read.xysfiles	Man page
read.xysfiles2	Man page
readSummaries	Man page
resids	Man page
residualSE	Man page
residualSE,oligoPLM-method	Man page
residuals,oligoPLM-method	Man page
rma	Man page
rma,ExonFeatureSet-method	Man page
rma,ExpressionFeatureSet-method	Man page
rma,GeneFeatureSet-method	Man page
rma,GenericFeatureSet-method	Man page
rma,HTAFeatureSet-method	Man page
rma,SnpCnvFeatureSet-method	Man page
rma-methods	Man page
runDate	Man page
runDate,FeatureSet-method	Man page
runDate-methods	Man page
se	Man page
se,oligoPLM-method	Man page
se.probe	Man page
se.probe,oligoPLM-method	Man page
seqColors	Man page
seqColors2	Man page
sequenceDesignMatrix	Man page
show,oligoPLM-method	Man page
snprma	Man page
summarizationMethods	Man page
summarize	Man page
summarize,ff_matrix-method	Man page
summarize,matrix-method	Man page
summarize-methods	Man page
weights,oligoPLM-method	Man page