Methods for fitting probe-level models

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Documentation for package ‘affyPLM’ version 1.28.5

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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