# Methods for fitting probe-level models

## Documentation for package `affyPLM' version 1.12.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A B C D F G I M N P R S T V W

## -- A --

annotation,PLMset-method | Class PLMset

## -- B --

bg.correct.LESN | LESN - Low End Signal is Noise Background corrections
boxplot,PLMset-method | Class PLMset

## -- C --

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<-,PLMset-method | Class PLMset

## -- D --

description,PLMset-method | Class PLMset

## -- F --

fitPLM | Fit a Probe Level Model to Affymetrix Genechip Data.

## -- G --

getCdfInfo,PLMset-method | Class PLMset

## -- I --

image,PLMset-method | Class PLMset
indexProbes,PLMset,character-method | Class PLMset
indexProbesProcessed | Class PLMset
indexProbesProcessed,PLMset-method | Class PLMset

## -- M --

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

## -- N --

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.quantiles.determine.target | Quantile Normalization using a specified target distribution vector
normalize.quantiles.in.blocks | Quantile Normalization carried out separately within blocks of rows
normalize.quantiles.use.target | Quantile Normalization using a specified target distribution vector
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

## -- P --

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 exprSet
preprocess | Background correct and Normalize
pset2eset | Convert a PLMset to an exprSet
pseudoColorBar | Coloring pseudo chip images
pseudoPalette | Coloring pseudo chip images

## -- R --

ReadRMAExpress | Read RMAExpress computed expression values
resid,PLMset-method | Class PLMset
resid<-,PLMset-method | Class PLMset
residSE | Class PLMset
residSE,PLMset-method | Class PLMset
residuals,PLMset-method | 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

## -- S --

sampleNames,PLMset-method | Class PLMset
sampleNames<-,PLMset-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<-,PLMset-method | Class PLMset
show,PLMset-method | Class PLMset
summary,PLMset-method | Class PLMset

## -- T --

threestep | Three Step expression measures
threestepPLM | Three Step expression measures returned as a PLMset

## -- V --

varcov | Class PLMset
varcov,PLMset-method | Class PLMset

## -- W --

weights,PLMset-method | Class PLMset
weights<-,PLMset-method | Class PLMset