Methods for fitting probe-level models

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Documentation for package ‘affyPLM’ version 1.85.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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