homedir="/amber1/scratch/temp/ririzarr/tcga/affy" dirs=list.files(homedir) batchNames=as.numeric(gsub("broad.mit.edu_OV.HT_HG-U133A.Level_1.|.1002.0","",dirs)) O=order(batchNames) dirs=dirs[O] batchNames=batchNames[O] library(affy) files=vector("list",length(dirs)) for(i in seq(along=dirs)){ tmpPath=file.path(homedir,dirs[i]) fns=list.files(tmpPath) files[[i]]=fns[grep("[cC][eE][lL]",fns)] } nfiles=sapply(files,length) starts=c(0,cumsum(nfiles[-length(nfiles)])) cnames=vector("character",sum(nfiles)) batch=factor(rep(seq(along=files),nfiles)) filenames=vector("character",sum(nfiles)) for(i in seq(along=dirs)){ tmpPath=file.path(homedir,dirs[i]) fns=files[[i]] filenames[starts[i]+seq(along=fns)]=file.path(tmpPath,fns) } ##No dates in the cel files!! what the f? ##dates=vector("character",(length(filenames))) ##for(i in seq(along=filenames)){ ## dates[i]=celfileDate(filenames[i]) ##} e=justRMA(filenames=filenames,celfile.path="/") mat=exprs(e) ##tmp=genefilter::rowFtests(mat,batch) save(mat,batch,batchNames,file="affy-expr.rda")