justPlier {plier}R Documentation

Implements the PLIER algorithm

Description

Provides a wrapper around Affymetrix's API to provide an implementation of the PLIER alogrimth

Usage

justPlier(eset=ReadAffy(),replicate=1:length(eset),get.affinities=FALSE,normalize=F,norm.type="together",augmentation=0.1,defaultaffinity=1.0,defaultconcentration=1.0,attenuation=0.005,seaconvergence=0.000001,seaiteration=3000,gmcutoff=0.15,probepenalty=0.001,concpenalty=0.000001,usemm=TRUE,usemodel=FALSE,fitaffinity=T,plierconvergence=0.000001,plieriteration=3000,dropmax=3.0,lambdalimit=0.01,optimization=0)

Arguments

eset An AffyBatch object containing the raw data
replicate A factor containing the replicate structure to use for grouping samples
get.affinities If TRUE, then return affinities in the preprocessing slot of the exprSet object
normalize If TRUE then apply quantile normalization to the probes before generating expression calls
norm.type Can be 'separate', 'pmonly', 'mmonly' or 'together'
augmentation Model parameter
defaultaffinity Model parameter
defaultconcentration Model parameter
attenuation Model parameter
seaconvergence Model parameter
seaiteration Model parameter
gmcutoff Model parameter
probepenalty Model parameter
concpenalty Model parameter
usemm Model parameter
usemodel Model parameter
fitaffinity Model parameter
plierconvergence Model parameter
plieriteration Model parameter
dropmax Model parameter
lambdalimit Model parameter
optimization Model parameter

Details

Value

An Expression set containing PLIER generated expression calls

Author(s)

Crispin J Miller (wrapper), Earl Hubbell (algorithm)

References

bioinf.picr.man.ac.uk www.affymetrix.com

See Also

normalize.AffyBatch.quantiles

Examples



[Package plier version 1.2.0 Index]