I just would like to report an error while reading .gpr with limma If I use: files<-dir(pattern="*\\.gpr") RG<-read.maimages(files,source='genepix') Read BG01.gpr Read BG02.gpr Read GE01.gpr Error in "[.data.frame"(obj, , columns$Rf) : undefined columns selected but if I read separatly:: RG.13<-read.maimages(files[1:3],source='genepix',wt.fun=wtflags(0.1)) RG.56<-read.maimages(files[5:6],source='genepix',wt.fun=wtflags(0.1)) RG.4<-read.maimages(files[4],source='genepix',wt.fun=wtflags(0)) RG<-cbind(RG.13,RG.4,RG.56) then it works. I also succeed reading the whole batch of files together with function from marray package. -- Mayte Suarez Farinas The Rockefeller University 1230 York Avenue, Box 212 New York, NY 10021 phone: 1-212-327-8186 fax: 1-212-327-7422