justPlier: Implements the PLIER algorithm
In plier: Implements the Affymetrix PLIER algorithm

Description Usage Arguments Details Value Author(s) References See Also

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=FALSE,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=TRUE,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 description@preprocessing slot of the ExpressionSet 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

This function is a thin wrapper around the Affymetrix implementation. For more details, including information about the meaning of the different model parameters, please see the plier documentation at www.affymetrix.com.

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

plier documentation built on Nov. 8, 2020, 7:49 p.m.