Dear BioConductor users, I am trying to analyze my Affy U133A chips (38 total) using the gcrma protocol but substituting loess instead of quantile normalization. I am doing this on a remote UNIX server using R 1.9.1 and BioConductor 1.4. I have already processed this dataset using >eset<- gcrma(dat) There was no problem at all. But when I substituted the QN for loess, it took almost 6 hours to complete the normalization! I ran into memory trouble after all the comparisons were done and got the error message (Failure to allocate a vector of ~145,000KB.) Is there any way of working around this problem? Because I used the expresso function in the following order-gcrma correction, pmonly, loess, and medianpolish. I suspect the memory failure is when R is trying to summarize the probesets. Can I summarize the probesets before doing loess normalization? That way the memory usage is less? Is the operation order still "legal"? Any suggestions will be great! Thank you for your time, Edmund Chang