annotation,PLMset-method	PLMset-class
bg.correct.gcrma	affyPLM-internal
bg.correct.LESN	bg.correct.LESN
bg.correct.shift	affyPLM-internal
bg.correct.stretch	affyPLM-internal
boxplot,PLMset-method	PLMset-class
cdfName,PLMset-method	PLMset-class
coefs	PLMset-class
coefs,PLMset-method	PLMset-class
coefs.const	PLMset-class
coefs.const,PLMset-method	PLMset-class
coefs.probe	PLMset-class
coefs.probe,PLMset-method	PLMset-class
coefs<-	PLMset-class
coefs<-,PLMset-method	PLMset-class
convert.LESN.param	affyPLM-internal
description,PLMset-method	PLMset-class
fitPLM	fitPLM
fitPLM.old	affyPLM-internal
get.background.code	affyPLM-internal
get.default.psi.k	affyPLM-internal
get.normalization.code	affyPLM-internal
get.psi.code	affyPLM-internal
get.summary.code	affyPLM-internal
getCdfInfo,PLMset-method	PLMset-class
image,PLMset-method	PLMset-class
indexProbes,PLMset,character-method	PLMset-class
indexProbesProcessed	PLMset-class
indexProbesProcessed,PLMset-method	PLMset-class
MAplot	MAplot
MAplot,PLMset-method	MAplot
Mbox	PLMset-class
Mbox,PLMset-method	PLMset-class
model.description	PLMset-class
model.description,PLMset-method	PLMset-class
normalize.AffyBatch.quantiles.chromosome	affyPLM-internal
normalize.AffyBatch.quantiles.probeset	normalize.quantiles.probeset
normalize.AffyBatch.scaling	normalize.scaling
normalize.ExpressionSet.contrasts	normalize.exprSet
normalize.ExpressionSet.invariantset	normalize.exprSet
normalize.ExpressionSet.loess	normalize.exprSet
normalize.ExpressionSet.methods	normalize.exprSet
normalize.ExpressionSet.qspline	normalize.exprSet
normalize.ExpressionSet.quantiles	normalize.exprSet
normalize.ExpressionSet.scaling	normalize.exprSet
normalize.scaling	normalize.scaling
normvec	PLMset-class
normvec,PLMset-method	PLMset-class
NUSE	PLMset-class
nuse	PLMset-class
NUSE,PLMset-method	PLMset-class
nuse,PLMset-method	PLMset-class
pData,PLMset-method	PLMset-class
pData<-,PLMset,data.frame-method	PLMset-class
phenoData,PLMset-method	PLMset-class
phenoData<-,PLMset,AnnotatedDataFrame-method	PLMset-class
PLM.designmatrix	affyPLM-internal
PLM.designmatrix2	affyPLM-internal
PLM.designmatrix3	affyPLM-internal
PLMset	PLMset-class
PLMset-class	PLMset-class
PLMset2exprSet	PLMset2exprSet
preprocess	preprocess
pset2eset	PLMset2exprSet
pseudoColorBar	pseudo
pseudoPalette	pseudo
ReadRMAExpress	ReadRMAExpress
resid,PLMset-method	PLMset-class
resid<-	PLMset-class
resid<-,PLMset-method	PLMset-class
residSE	PLMset-class
residSE,PLMset-method	PLMset-class
residuals,PLMset-method	PLMset-class
residuals<-	PLMset-class
residuals<-,PLMset-method	PLMset-class
RLE	PLMset-class
RLE,PLMset-method	PLMset-class
rmaPLM	rmaPLM
sampleNames,PLMset-method	PLMset-class
sampleNames<-	PLMset-class
sampleNames<-,PLMset,character-method	PLMset-class
se	PLMset-class
se,PLMset-method	PLMset-class
se.const	PLMset-class
se.const,PLMset-method	PLMset-class
se.probe	PLMset-class
se.probe,PLMset-method	PLMset-class
se<-	PLMset-class
se<-,PLMset-method	PLMset-class
show,PLMset-method	PLMset-class
summary,PLMset-method	PLMset-class
threestep	threestep
threestepPLM	threestepPLM
varcov	PLMset-class
varcov,PLMset-method	PLMset-class
verify.bg.param	affyPLM-internal
verify.constraint.types	affyPLM-internal
verify.model.param	affyPLM-internal
verify.norm.param	affyPLM-internal
verify.output.param	affyPLM-internal
verify.variable.types	affyPLM-internal
weights,PLMset-method	PLMset-class
weights<-	PLMset-class
weights<-,PLMset-method	PLMset-class