justPlier {plier} | R Documentation |
Provides a wrapper around Affymetrix's API to provide an implementation of the PLIER alogrimth
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)
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 |
An Expression set containing PLIER generated expression calls
Crispin J Miller (wrapper), Earl Hubbell (algorithm)
bioinf.picr.man.ac.uk www.affymetrix.com
normalize.AffyBatch.quantiles