Dear list I tried to run the qc function from simpleaffy on a an object consisting of 70 U133A arrays However, qc returned an error message indicating problems with allocating enough memory. I had set --max-mem-size = 2000Mb. What could I do about this? sessionInfo() Version 2.3.1 (2006-06-01) i386-pc-mingw32 attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: simpleaffy genefilter survival affyPLM gcrma matchprobes "2.6.0" "1.10.1" "2.26" "1.8.0" "2.4.1" "1.4.0" affydata affy affyio Biobase RWinEdt "1.8.0" "1.10.0" "1.0.0" "1.10.1" "1.7-4" Cheers Per Broberg

Hi Per, Per.Broberg at astrazeneca.com wrote: > Dear list > > I tried to run the qc function from simpleaffy on a an object consisting of > 70 U133A arrays > > However, qc returned an error message indicating problems with allocating > enough memory. I had set --max-mem-size = 2000Mb. > > What could I do about this? Windows is problematic in that large chunks of RAM are often not available for use even if they have been freed up. You might need to do an iterative process. First do all the steps you need to do prior to the call to qc(). Then save only those objects you will need for the qc() step (using the save() function), then quit R, restart, load() the saved objects, and try the qc() step. If that doesn't work, you just need more RAM. On windows, you can go up to 4 Gb, but you will then need to make R 'large address aware'. I forget how you do that, but a simple google search or RSiteSearch() should come up with something. Unfortunately, you will still only be able to use maybe 3 Gb of your RAM, but that may be sufficient. If that still doesn't work, you could try Linux (you can do a quick attempt using Quantian, which boots from CD and has R and BioC installed), which is much better at handling memory than windows. If that still doesn't work, then you may have to get a 64 bit operating system and > 4Gb RAM. Best, Jim > > sessionInfo() > Version 2.3.1 (2006-06-01) > i386-pc-mingw32 > > attached base packages: > [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" > [7] "utils" "datasets" "base" > > other attached packages: > simpleaffy genefilter survival affyPLM gcrma matchprobes > "2.6.0" "1.10.1" "2.26" "1.8.0" "2.4.1" "1.4.0" > affydata affy affyio Biobase RWinEdt > "1.8.0" "1.10.0" "1.0.0" "1.10.1" "1.7-4" > > > Cheers > > > Per Broberg > > _______________________________________________ > 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.