I am sorry, I think that the attachments didn't make it. Here is the R script with the ResetEnvir and RemoveProbes function implementations. The first function just load the cdf and probe packages, and if necessary, detaches previously installed ones. The second one does the job. As it modifies the cdf and probe environment used by affy to access probe level info it should work with any algorithm implemented in affy + gcrma + affyPLM packages (I tested it on mas, rma, rmaPLM, and gcrma). Please be aware of the behavior of different versions of GCRMA reported in my previous post to the list. Regards, A./ # # ResetEnvir # goal:Detach, if necessary, cdf and probe environments, # and (re)load them. # in : # cdfpackagename (e.g. "hgu95av2cdf") # probepackagename (e.g. "hgu95av2probe") # out : --- # ResetEnvir<-function(cdfpackagename,probepackagename){ ll<-search() cdfpackagepos <- grep(cdfpackagename,ll) if(length(cdfpackagepos)>0) detach(pos=cdfpackagepos) ll<-search() probepackagepos <- grep(probepackagename,ll) if(length(probepackagepos)>0) detach(pos=probepackagepos) library(cdfpackagename,character.only=T) library(probepackagename,character.only=T) } # # RemoveProbes # goal: Modification of CDF and PROBE environments # in : # listOutProbes: list of probes to be removed from cdf and probe # environments (e.g. c("1001_at1","1032_at6"). # If NULL no probe will be taken out. # listOutProbeSets: list of probesets to be removed from cdf and probe # environments (e.g. c("1006_at","1032_f_at"). # If NULL no probeset will be removed. # cdfpackagename: (e.g. "hgu95av2cdf") # probepackagename: (e.g. "hgu95av2probe") # destructive: unimplemented option, see NOTE # # out : --- # # NOTE 1: After a call to RemoveProbes the probenames reported by # pm and mm accessing functions implemented in the affy package, will # be in general differents from the original ones in probesets where # probes have been removed. This happens as in this functions the probe names # are always assigned sequentially. # RemoveProbes modifies the specified CDF and PROBE environments # in a consistent BUT destructive way. Take this in consideartion if # your code relays on absolute references to probe names. # # A chunk of code to illustrate this # # library(affy) # library(affydata) # source("removeProbes.R") # # data(Dilution) # Dilution@cdfName<-"hgu95av2" # fix cdf name # # cleancdf <- cleancdfname(Dilution@cdfName,addcdf=FALSE) # cdfpackagename <- paste(cleancdf,"cdf",sep="") # probepackagename <- paste(cleancdf,"probe",sep="") # # ResetEnvir(cdfpackagename,probepackagename) # pm(Dilution,"1000_at") # as.data.frame(get(probepackagename))[1:16,1:4] # # RemoveProbes(c("1000_at2"),NULL,cdfpackagename,probepackagename) # pm(Dilution,"1000_at") # as.data.frame(get(probepackagename))[1:15,1:4] # # NOTE2 : See my April 20 post to BioC mailing list (and eventually its # continuation) regarding differences reported # between GCRMA 1.1.0 and GCRMA 1.1.3 # RemoveProbes<-function(listOutProbes=NULL, listOutProbeSets=NULL, cdfpackagename,probepackagename,destructive=TRUE){ #default probe dataset values probe.env.orig <- get(probepackagename) if(!is.null(listOutProbes)){ # taking probes out from CDF env probes<- unlist(lapply(listOutProbes,function(x){ a<-strsplit(x,"at") aux1<-paste(a[[1]][1],"at",sep="") aux2<-as.integer(a[[1]][2]) c(aux1,aux2) })) n1<-as.character(probes[seq(1,(length(probes)/2))*2-1]) n2<-as.integer(probes[seq(1,(length(probes)/2))*2]) probes<-data.frame(I(n1),n2) probes[,1]<-as.character(probes[,1]) probes[,2]<-as.integer(probes[,2]) pset<-unique(probes[,1]) for(i in seq(along=pset)){ ii <-grep(pset[i],probes[,1]) iout<-probes[ii,2] a<-get(pset[i],env=get(cdfpackagename)) a<-a[-iout,] assign(pset[i],a,env=get(cdfpackagename)) } } # taking probesets out from CDF env if(!is.null(listOutProbeSets)){ rm(list=listOutProbeSets,envir=get(cdfpackagename)) } # setting the PROBE env accordingly (idea from gcrma compute.affinities.R) tmp <- get("xy2i",paste("package:",cdfpackagename,sep="")) newAB <- new("AffyBatch",cdfName=cleancdf) pmIndex <- unlist(indexProbes(newAB,"pm")) subIndex<- match(tmp(probe.env.orig$x,probe.env.orig$y),pmIndex) rm(newAB) iNA <- whichis.na(subIndex)) if(length(iNA)>0){ ipos<-grep(probepackagename,search()) assign(probepackagename,probe.env.orig[-iNA,],pos=ipos) } } 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