# Methods for fitting probe-level models

## Documentation for package ‘affyPLM’ version 1.30.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

annotation-method | Class PLMset
bg.correct.LESN | LESN - Low End Signal is Noise Background corrections
boxplot-method | Class PLMset
cdfName-method | Class PLMset
coefs | Class PLMset
coefs-method | Class PLMset
coefs.const | Class PLMset
coefs.const-method | Class PLMset
coefs.probe | Class PLMset
coefs.probe-method | Class PLMset
coefs<- | Class PLMset
coefs<--method | Class PLMset
description-method | Class PLMset
fitPLM | Fit a Probe Level Model to Affymetrix Genechip Data.
getCdfInfo-method | Class PLMset
image-method | Class PLMset
indexProbes-method | Class PLMset
indexProbesProcessed | Class PLMset
indexProbesProcessed-method | Class PLMset
MAplot | Relative M vs. A plots
MAplot-method | Relative M vs. A plots
Mbox | Class PLMset
Mbox-method | Class PLMset
model.description | Class PLMset
model.description-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-method | Class PLMset
NUSE | Class PLMset
nuse | Class PLMset
NUSE-method | Class PLMset
nuse-method | Class PLMset
pData-method | Class PLMset
pData<--method | Class PLMset
phenoData-method | Class PLMset
phenoData<--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-method | Class PLMset
resid<- | Class PLMset
resid<--method | Class PLMset
residSE | Class PLMset
residSE-method | Class PLMset
residuals | Class PLMset
residuals-method | Class PLMset
residuals<- | Class PLMset
residuals<--method | Class PLMset
RLE | Class PLMset
RLE-method | Class PLMset
rmaPLM | Fit a RMA to Affymetrix Genechip Data as a PLMset
sampleNames-method | Class PLMset
sampleNames<- | Class PLMset
sampleNames<--method | Class PLMset
se | Class PLMset
se-method | Class PLMset
se.const | Class PLMset
se.const-method | Class PLMset
se.probe | Class PLMset
se.probe-method | Class PLMset
se<- | Class PLMset
se<--method | Class PLMset
show-method | Class PLMset
summary-method | Class PLMset
threestep | Three Step expression measures
threestepPLM | Three Step expression measures returned as a PLMset
varcov | Class PLMset
varcov-method | Class PLMset
weights | Class PLMset
weights-method | Class PLMset
weights<- | Class PLMset
weights<--method | Class PLMset