Hi Tae-Hoon, I am very surprise by your answers :
When I try to make an affybatch with bioconductor and R 1.9.1, I was unable to read and normalise more than 80 HU-133A CEL file with a Linux 32 bits computer and 4 GB of RAM + 8 GB of swap (Of course, without any other process on the computer and I don't' want do to "JustRMA" because I want the probe level information in the affybatch, And it's not a limit in R configuration, because if I follow the memory usage during the R session, R is using all the 4GB RAM memory (the swap is not use) before the memory error) For this raison we are planning to buy a 64 bits under Linux, but, if with Mac OS X and 1.5 GB of RAM, we can solve this problem, I will buy a Mac and not a linux 64 bits computer. So, what kind of normalization are you doing ? Some one with bioconductor and the affy package or an other one ? Could you precise ? For the other R & BioC : Do you think that there is a difference between linux and MacOS for the memory management under R ? What is a "good" hardward solution for "R / Linux 64 bits" ? Thanks for your help. laurent -----Message d'origine----- De : [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] De la part de Tae-Hoon Chung Envoye : vendredi 2 juillet 2004 01:52 A : Kort, Eric Cc : [EMAIL PROTECTED] Objet : Re: [R] Absolute ceiling on R's memory usage = 4 gigabytes? Hi, Eric. It seems a little bit puzzling to me. Which Affymetrix chip do you use? The reason I'm asking this is that yesterday I was able to normalize 150 HU-133A CEL files (containing 22283 probes) using R 1.9.1 in Mac OS X 10.3.3 with 1.5 GB memory. If your chip has more probes than this, then it must be understandable ... On Jul 1, 2004, at 2:59 PM, Kort, Eric wrote: > Hello. By way of background, I am running out of memory when > attempting to normalize the data from 160 affymetrix microarrays using > justRMA (from the affy package). This is despite making 6 gigabytes > of swap space available on our sgi irix machine (which has 2 gigabytes > of ram). I have seen in various discussions statements such as "you > will need at least 6 gigabytes of memory to normalize that many > chips", but my question is this: > > I cannot set the memory limits of R (1.9.1) higher than 4 gigabytes as > attempting to do so results in this message: > > WARNING: --max-vsize=4098M=4098`M': too large and ignored > > I experience this both on my windows box (on which I cannot allocate > more than 4 gigabytes of swap space anyway), and on an the above > mentioned sgi irix machine (on which I can). In view of that, I do > not see what good it does to make > 4 gigabytes of ram+swap space > available. Does this mean 4 gigabytes is the absolute upper limit of > R's memory usage...or perhaps 8 gigabytes since you can set both the > stack and the heap size to 4 gigabytes? > > Thanks, > Eric > > > This email message, including any attachments, is for the > so...{{dropped}} > > ______________________________________________ > [EMAIL PROTECTED] mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > > Tae-Hoon Chung, Ph.D Post-doctoral Research Fellow Molecular Diagnostics and Target Validation Division Translational Genomics Research Institute 1275 W Washington St, Tempe AZ 85281 USA Phone: 602-343-8724 ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html