Here is a small script to illustrate how RemoveProbes works, library(affydata) source("removeProbes.R") data(Dilution) Dilution@cdfName<-"hgu95av2" #fix cdf name # # 'offending' probes and probesets # #listOutProbes =c("1000_at1","1000_at3","1001_at2","1001_at8","1001_at9") #listOutProbeSets=c("1002_f_at","1003_s_at","1004_at") listOutProbes =c("1000_at1") listOutProbeSets=NULL require(gcrma) # # Load CDF and PROBE environments # cleancdf <- cleancdfname(Dilution@cdfName,addcdf=FALSE) cdfpackagename <- paste(cleancdf,"cdf",sep="") probepackagename <- paste(cleancdf,"probe",sep="") # load cdf and probe packages detaching, if necessary, # previously loaded ones. ResetEnvir(cdfpackagename,probepackagename) #mas5.0, rma and gcrma calculation with the full set of probes d.rma <-rma(Dilution) d.gcrma<-gcrma(Dilution) d.mas <-mas5(Dilution) d.mas.call<-mas5calls(Dilution) # # CDF and PROBE modifications # RemoveProbes(listOutProbes,listOutProbeSets,cdfpackagename,probepackag en ame) #mas 5.0, rma and gcrma calculations without offending probes d.rma.out <-rma(Dilution) d.gcrma.out<-gcrma(Dilution) d.mas.out <-mas5(Dilution) d.mas.call.out <-mas5calls(Dilution) layout(matrix(c(1,2,3,4),2,2),1,1) plot(exprs(d.rma)[,1],exprs(d.rma.out)[,1],pch=".", xlim=c(7.5,8.5),ylim=c(7.5,8.5),main="RMA") points(exprs(d.rma)[1,1],exprs(d.rma.out)[1,1],col="red") plot(exprs(d.gcrma)[,1],exprs(d.gcrma.out)[,1], xlim=c(3,10),ylim=c(3,10),pch=".",main="GCRMA") points(exprs(d.gcrma)[1,1],exprs(d.gcrma.out)[1,1],col="red") plot(log2(exprs(d.mas))[,1],log2(exprs(d.mas.out))[,1],pch=".",main="M AS 5.0", xlim=c(9,10),ylim=c(9,10),log="xy") points(log2(exprs(d.mas))[1,1],log2(exprs(d.mas.out))[1,1],col="red") 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