If you are planning on using that number of chips, at the moment the only recourse is to use a 64 bit architecture which will allow you to use more than 4 Gb RAM. Even using justRMA I bet you will not be able to do more than 50 - 60 of the version 2 chips with only 1 Gb RAM. Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Li, Aiguo (NIH/NCI)" <liai@mail.nih.gov> 06/29/04 5:53 PM >>> Hi all. My name is AG LEE, a new bioconductor user. Our project is using HG_U133 plus 2 chips which contain approximately 56,000 probes and the .cel file in text format is about 32MB. Currently we have more than 100 chips and number is growing quickly. I tried to get the data into bioconductor using ReadAffy and can only read in 19 chips before it run out of memory (my machine has 1 GB memory). I tried to normalize the data using "expresso(d, normalize.method ="invariantset", bg.correct = FALSE, pmcorrect.method="pmonly", summary.method="liwong"" and it ran out of memory before the completion. I have option to upgrade my memory to 4GB, but still concern whether it will really help when our chips number reaches several hundres or thousands. Does anybody can help me with some suggestions? Thanks in advance. AG LEE [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor