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

The fast transformation uses an ad hoc procedure. When the intensities are very close to what appear to be background level, they are adjusted towards a small constant. So it is possible for some probes to get a bigger number after the transformation. On Fri, 10 Sep 2004, Ariel Chernomoretz wrote: > 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 > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >