# Methods for fitting probe-level models

## Documentation for package ‘affyPLM’ version 1.22.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

annotation,PLMset-method | Class PLMset
bg.correct.LESN | LESN - Low End Signal is Noise Background corrections
boxplot,PLMset-method | Class PLMset
cdfName,PLMset-method | Class PLMset
coefs | Class PLMset
coefs,PLMset-method | Class PLMset
coefs.const | Class PLMset
coefs.const,PLMset-method | Class PLMset
coefs.probe | Class PLMset
coefs.probe,PLMset-method | Class PLMset
coefs<- | Class PLMset
coefs<-,PLMset-method | Class PLMset
description,PLMset-method | Class PLMset
fitPLM | Fit a Probe Level Model to Affymetrix Genechip Data.
getCdfInfo,PLMset-method | Class PLMset
image,PLMset-method | Class PLMset
indexProbes,PLMset,character-method | Class PLMset
indexProbesProcessed | Class PLMset
indexProbesProcessed,PLMset-method | Class PLMset
MAplot | Relative M vs. A plots
MAplot,PLMset-method | Relative M vs. A plots
Mbox | Class PLMset
Mbox,PLMset-method | Class PLMset
model.description | Class PLMset
model.description,PLMset-method | Class PLMset
normalize.AffyBatch.quantiles.probeset | Quantile Normalization applied to probesets
normalize.AffyBatch.scaling | Scaling normalization
normalize.ExpressionSet.contrasts | Normalization applied to ExpressionSets
normalize.ExpressionSet.invariantset | Normalization applied to ExpressionSets
normalize.ExpressionSet.loess | Normalization applied to ExpressionSets
normalize.ExpressionSet.methods | Normalization applied to ExpressionSets
normalize.ExpressionSet.qspline | Normalization applied to ExpressionSets
normalize.ExpressionSet.quantiles | Normalization applied to ExpressionSets
normalize.ExpressionSet.scaling | Normalization applied to ExpressionSets
normalize.scaling | Scaling normalization
normvec | Class PLMset
normvec,PLMset-method | Class PLMset
NUSE | Class PLMset
nuse | Class PLMset
NUSE,PLMset-method | Class PLMset
nuse,PLMset-method | Class PLMset
pData,PLMset-method | Class PLMset
pData<-,PLMset,data.frame-method | Class PLMset
phenoData,PLMset-method | Class PLMset
phenoData<-,PLMset,AnnotatedDataFrame-method | Class PLMset
PLMset | Class PLMset
PLMset-class | Class PLMset
PLMset2exprSet | Convert a PLMset to an ExpressionSet
preprocess | Background correct and Normalize
pset2eset | Convert a PLMset to an ExpressionSet
pseudoColorBar | Coloring pseudo chip images
pseudoPalette | Coloring pseudo chip images
ReadRMAExpress | Read RMAExpress computed expression values
resid | Class PLMset
resid,PLMset-method | Class PLMset
resid<- | Class PLMset
resid<-,PLMset-method | Class PLMset
residSE | Class PLMset
residSE,PLMset-method | Class PLMset
residuals | Class PLMset
residuals,PLMset-method | Class PLMset
residuals<- | Class PLMset
residuals<-,PLMset-method | Class PLMset
RLE | Class PLMset
RLE,PLMset-method | Class PLMset
rmaPLM | Fit a RMA to Affymetrix Genechip Data as a PLMset
sampleNames,PLMset-method | Class PLMset
sampleNames<- | Class PLMset
sampleNames<-,PLMset,character-method | Class PLMset
se | Class PLMset
se,PLMset-method | Class PLMset
se.const | Class PLMset
se.const,PLMset-method | Class PLMset
se.probe | Class PLMset
se.probe,PLMset-method | Class PLMset
se<- | Class PLMset
se<-,PLMset-method | Class PLMset
show,PLMset-method | Class PLMset
summary,PLMset-method | Class PLMset
threestep | Three Step expression measures
threestepPLM | Three Step expression measures returned as a PLMset
varcov | Class PLMset
varcov,PLMset-method | Class PLMset
weights | Class PLMset
weights,PLMset-method | Class PLMset
weights<- | Class PLMset
weights<-,PLMset-method | Class PLMset