Dear Bioconductors, I am trying to read and normalize 230 microarray CEL files (Affy U133A). This is obviously very difficult since it requires a lot of RAM and always fails with an alloc error. I tested it on a dual Xeon (2.3Ghz) linux machine with 4Gb of RAM, but failed at the ReadAffy command. Except from finding a high-end machine with lots of RAM and CPU power, is there a way to run this on a normal computer? Theoretically, it should be possible to read and write to hard-drive. I don't mind if it takes 2 or 3 days, just as long as it will possible to do. Is there a way to break down ReadAffy and gcrma to smaller subsets and then combine them to one matrix of genes x samples? Anybody knows how GNF was processed and normalized? (158 arrays) Thanks for the help, Yair

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Hi Yair, Yair Benita wrote: > Dear Bioconductors, > I am trying to read and normalize 230 microarray CEL files (Affy U133A). > This is obviously very difficult since it requires a lot of RAM and always > fails with an alloc error. I tested it on a dual Xeon (2.3Ghz) linux machine > with 4Gb of RAM, but failed at the ReadAffy command. > > Except from finding a high-end machine with lots of RAM and CPU power, is > there a way to run this on a normal computer? > Theoretically, it should be possible to read and write to hard- drive. I > don't mind if it takes 2 or 3 days, just as long as it will possible to do. I know someone who just did around 1000 U133 Plus 2 chips using a Linux box with 16 Gb RAM using justRMA(), so I am betting you can do all 230 with your comp. The downside of this is you won't be able to do many QC plots. HTH, Jim > > Is there a way to break down ReadAffy and gcrma to smaller subsets and then > combine them to one matrix of genes x samples? > > Anybody knows how GNF was processed and normalized? (158 arrays) > > Thanks for the help, > Yair > > _______________________________________________ > 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

On Monday 18 December 2006 14:05, Yair Benita wrote: > Dear Bioconductors, > I am trying to read and normalize 230 microarray CEL files (Affy U133A). > This is obviously very difficult since it requires a lot of RAM and always > fails with an alloc error. I tested it on a dual Xeon (2.3Ghz) linux > machine with 4Gb of RAM, but failed at the ReadAffy command. I haven't tried it, but justGCRMA and justRMA are designed to be memory-efficient. Have you tried either of those? > Anybody knows how GNF was processed and normalized? (158 arrays) They are available here (http://wombat.gnf.org/index.html) as either gcRMA or MAS5 normalized. Also, the raw data are available from them as .CEL files. You can contact them and they will even send you a DVD, if I recall. Sean