| Title: | Implements the Affymetrix PLIER algorithm |
|---|---|
| Description: | The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values. |
| Authors: | Affymetrix Inc., Crispin J Miller, PICR |
| Maintainer: | Crispin Miller <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.77.0 |
| Built: | 2024-10-31 04:34:47 UTC |
| Source: | https://github.com/bioc/plier |
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)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