Methods for fitting probe-level models


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Documentation for package `affyPLM' version 1.12.0

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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