[BioC] gcrma background

[Ariel Chernomoretz]

Hi all,
I just started to work with gcrma and  I have a question regarding the 
background substracted values obtained with 'gcrma.engine'. If I 
compare the corrected pm values against the original ones I found that 
some of them (~20%) get bigger values after the correction . I did not 
expected that. I guess I am doing something wrong here but I do not 
realize what. Any help would be appreciate


I compare:   pm.Data.gcrmabkg[,1] vs. pm(Data)[,1]
using:
pm.Data.gcrmabkg<-myGCRMA.background(Data,stype="affinities")
myGCRMA.background<-function(ddata,affin=NULL,
			gOptical = TRUE,
			sType    = "fullmodel",
			bFast    = TRUE,
			fK       = 6*bFast+0.5*(1-bFast),
			fStretch = 1.15*bFast+1*(1-bFast),
			bVerbose = TRUE,
			fRho     = 0.7)
{

  require(affy,quietly=TRUE)
  require(gcrma,quietly=TRUE)

  if(class(affin)=="NULL"){
   affin<-compute.affinities(annotation(ddata))
   affin.new<<-affin
  }
  pm.affinities <- pm(affin)
  mm.affinities <- mm(affin)

  if(gOptical){
   ddata = bg.adjust.optical(ddata)
  }

  pms<-pm(ddata)
  mms<-mm(ddata)

  ppm <- gcrma.engine(pms=pms,
                     mms=mms,
		    pm.affinities=pm.affinities,
		    mm.affinities=mm.affinities,
		    type=sType,
		    k=fK,
		    stretch=fStretch,
		    correction=1,
		    rho=fRho,
		    verbose=bVerbose,
		    fast=bFast)
  return(ppm)
}






Ariel Chernomoretz, Ph.D.
Centre de recherche du CHUL
2705 Blv Laurier, bloc T-367
Sainte-Foy, Qc
G1V 4G2
(418)-525-4444 ext 46339