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The error is because you don't have enough memory to process that many chips. There are no tricks needed. You just need to buy more RAM. Best, Jim JONG-MIN LEE wrote: > Hi, all, > Please help me with justgcRMA memory problem. > Supposedly, justGCRMA use less memory, but it couldn't process ~60 arrays. > I am using Windows XP with 2GB memory, fresh R session, no other programs > running, R2.4.1, BioC1.9. > It works fine with about 55 arays of U133+2, but it couldn't read arrays > beyond that with memory error. > I know there are a lot of this kind messages, but I couldn't find a real > solution. > I tried all different things for example, --max-mem-size stuff, and newer > version of R (2.6.1). > Dos any one know any trick? > Thanks. > JongMin > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

The aroma.affymetrix package, which was designed to process virtually any number of arrays, can do gcRMA background correction. Follow http://www.braju.com/R/aroma.affymetrix/ and see Page 'Calibration and normalization of probe-level data'. There are also (brief) instruction on what annotation files you need. For further questions, please post your questions on the package's mailing list. /H On 08/01/2008, JONG-MIN LEE <dungras at="" gmail.com=""> wrote: > Hi, all, > Please help me with justgcRMA memory problem. > Supposedly, justGCRMA use less memory, but it couldn't process ~60 arrays. > I am using Windows XP with 2GB memory, fresh R session, no other programs > running, R2.4.1, BioC1.9. > It works fine with about 55 arays of U133+2, but it couldn't read arrays > beyond that with memory error. > I know there are a lot of this kind messages, but I couldn't find a real > solution. > I tried all different things for example, --max-mem-size stuff, and newer > version of R (2.6.1). > Dos any one know any trick? > Thanks. > JongMin > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >