Tristan, I have a soft spot for problems analyzing microarrays with R.. for the memory issue, there have been previous posts to this list.. But here is the answer I gave a few weeks ago. If you need more memory, you have to move to linux or recompile R for windows yourself.. .. But you'll still need a computer with more memory. The long term solution, which we are implementing, is to rewrite the normalization code so it doesn't Need to load all those arrays at once.
-- cut previous part of message-- The defaults in R is to play nice and limit your allocation to half the available RAM. Make sure you have a lot of disk swap space (at least 1G with 2G of RAM) and you can set your memory limit to 2G for R. See help(memory.size) and use the memory.limit function Hugues P.s. Someone let me use their 16Gig of RAM linux And I was able to run R-64 bits with "top" showing 6Gigs of RAM allocated (with suitable --max-mem-size command line parameters at startup for R). -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Benilton Carvalho Sent: Thursday, February 01, 2007 6:47 PM To: Tristan Coram Cc: R-help@stat.math.ethz.ch Subject: Re: [R] Affymetrix data analysis The bioconductor mailing list is probably a better place to ask this type of question. [EMAIL PROTECTED] But we also need to know what arrays are you working with, what the errors are, what your sessionInfo() is.... Let us know, ok? b On Feb 1, 2007, at 5:46 PM, Tristan Coram wrote: > Hi, > > > > I am trying to read in my Affymetrix CEL files (48 files, total > ~600 MB) but > I keep getting memory errors. Can somebody please help me with > this. Or is > therea remote server I can send my data to for computation? > > > > Any help is much appreciated. > > > > Thanks > > > > > > Dr. Tristan Coram > > Postdoctoral Research Associate > > Research Plant Pathologist/Geneticist > > > > United States Department of Agriculture > > Agricultural Research Service > > Wheat Genetics, Quality Physiology & Disease Research > > > > 209 Johnson Hall > > Washington State University > > Pullman, WA 99163 > > > > Office: +1 509 335-1596 Fax: +1 509 335-2553 > > Email: [EMAIL PROTECTED] > > > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
