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Have you tried using justRMA() or justGCRMA()? These are two functions, which are supposed to take less memory (since they were written in C, if I recall correctly). Yours, Uri David Akavia Chen Li wrote: > Dear users, > > I often encounter memory problems when I use rma or gcrma to > analyze Affymetrix genechip data (i.e. hgu133atag, 22300 genes and 42