hi! For those having memory problems with the affy package: James MacDonald has contributed the function justRMA that computes a pm-only rma without creating an AffyBatch. It reads in cel files and returns exprSets. It wil be available in the next release. However, if you need it now, it is in the development version. if the devel version gives you trouble, as a last resort, use the rma package that adds it to whatever version you have now: http://www.biostat.jhsph.edu/~ririzarr/affy/index.html Note1: the "official" code for RMA is still in the affy rma funciton but if this can't handle your large data-set try justRMA. Note2: you dont need to use ReadAffy. a typical call may be library(affy) eset <- justRMA(widget=TRUE) ##or if you dont choose cel files: justRMA()