Hi. R should never crash, that's true. What's your version of R? Are you running R v.2.2.1? Then try to download the latest "patched" version. Are you running R v2.3.0 devel? Then try to download a newer version, because bugs get introduced once in a while in the devel version which are fixed a few days later. Troubleshooting: When does it crash? In the read.table() call? Try to narrow it down. If it is a memory problem, you can always try to through in a gc() in the end of your for loop. Also, if you're only interested in a few of the columns, you can the read.table() to ignore all others. See the help and argument 'colClasses'. That will speed up your reading and decrease the memory usage. R should still not crash, but you might avoid the bug this way. In your script, 'Count' and 'count' are two different objects! Also, your 'assign(print(i,quote=FALSE),x)' statement is very misleading (although correct). It's better to split it up in two lines: print(i,quote=FALSE); assign(i,x); /Henrik On 3/31/06, Hao Liu <liuha at="" umdnj.edu=""> wrote: > Dear All: > > I encountered this several times, could someone point out where the problem > is? I don't think it is the memory restriction or something... > > I have 345 MAS5 results formated as: probeset_id, expression_value, PA_call > in 345 text file. I tried to combine them into one single file, but only > retain one probeset_ID column. > > This is my commend: > > Files<-list.files(pattern=".txt$"); > Count<-0; > for(i in files) {x<-read.table(i, header=TRUE,sep="\t"); assign(print(i, > quote=FALSE),x);if(count==0){combined<-x;rm(x);count<-count+1;} else > {combined<-cbind(combined,x[,2:3]);rm(x);count<-count+1;}} > > After processing over 200 files, the program crashes. > > Is there a better way to get it done? And, for this large dataset, if I > don't want to use RMA -- which is easier to get using justrma, I am stuck > here... > > Thanks > Hao > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Henrik Bengtsson Mobile: +46 708 909208 (+2h UTC)