library(affy) tab=read.csv("bladdercels/bladdertab.csv",as.is=TRUE) eset=justRMA(filenames=tab$filename,celfile.path="bladdercels/") library(genefilter) outcome=tab[,8] bt=tab[,5] Index=which(outcome=="sTCC") Cplus=grep("CIS",bt[Index]) outcome[Index]="sTCC-CIS" outcome[Index[Cplus]]="sTCC+CIS" outcome[49:57]<-"Biopsy" mat=exprs(eset) dates=vector("character",ncol(mat)) for(i in seq(along=dates)){ tmp=affyio::read.celfile.header(file.path("bladdercels",tab$filenam[i]),info="full")$DatHeader dates[i]=strsplit(tmp,"\ +")[[1]][8] } dates=as.Date(dates,"%m/%d/%Y") batch=dates-min(dates); batch=as.numeric(cut(batch,c(-1,10,75,200,300,500))) save(mat,outcome,batch,dates,file="bladder-cancer.rda")