Sorry this has come up many times and I have looked for an answer in the mail archives, but I couldn?t find anything regarding amount of memory for many U133plus arrays. I have 60 U133plus2.0 arrays and I wanted to do some NUSE plots, but I can?t even read in the arrays using ReadAffy() and I know fitPLM() is more demanding. I am running R 2.0.1 and affy 1.5 on a Pentium 4 with Windows 2000 OS, 1G RAM. I tried increasing the memory by memory.limit(700000) but still get the error "cannot allocate vector of size 635107 any suggestions?? thanks, David

kfbargad@lg.ehu.es wrote: > Sorry this has come up many times and I have looked for an answer in > the mail archives, but I couldn?t find anything regarding amount of > memory for many U133plus arrays. > > I have 60 U133plus2.0 arrays and I wanted to do some NUSE plots, but I > can?t even read in the arrays using ReadAffy() and I know fitPLM() is > more demanding. > > I am running R 2.0.1 and affy 1.5 on a Pentium 4 with Windows 2000 OS, > 1G RAM. I tried increasing the memory by > > memory.limit(700000) You should append --max-mem-size=1000M to the target field of the shortcut you use to start R. This will still not allow you to read in and process 60 of the 133plus2 chips. I have 2 Gb and I bet I would have trouble with that many chips. You will likely need to increase the RAM in your computer, and would probably be better off using Linux, as the memory management appears to be much better on that OS. Note you don't have to install Linux on your comp; you can use Quantian which boots Linux off a CD and has R and BioC available. If all you need are expression values, look at ?justRMA which will be able to process all 60 chips with only 1 Gb RAM. HTH, Jim > > but still get the error "cannot allocate vector of size 635107 > > any suggestions?? > > thanks, > > David > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- 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