Hi, when analyzing more than 25 Affymetrix HGU133plus2 arrays the analysis fails during background correction with GCRMA and the error message says "cannot allocate vector of 301.000kB ...." I got the message ot only from my PC but also form a more potent computer (Ml570 G2, 4 CPU XEON MP 2.5/1Mb, 16 Gb RAM, s.o. RH AS 4.0). It does not appear that the computer is using all the memory available. After my actual 30 arrays I must analyze 380, which problems will I face? Any help? Thanx, Uli

Ulrich, Only on machines with 64 bit CPUs (e.g. Opteron) you can allocate more than 2-3 GB of RAM to a single process. Your Xeon CPUs are 32 bit which have a 'physical' memory limit. It is a nice machine to dedicate lots of memory to multiple processes, but never much more than 2 GB to a single one no matter what operating system you are using. Upgrading your tetrad board to 64 bit may be more pricy than getting a new single or dual 64 bit CPU (e.g. Opteron, MacG5) workstation with a unix type operating system (e.g. Linux, Mac OSX). Thomas On Fri 06/23/06 14:53, Ulrich Pfeffer wrote: > Hi, > > when analyzing more than 25 Affymetrix HGU133plus2 arrays the analysis > fails during background correction with GCRMA and the error message says > "cannot allocate vector of 301.000kB ...." > > I got the message ot only from my PC but also form a more potent computer > (Ml570 G2, 4 CPU XEON MP 2.5/1Mb, > 16 Gb RAM, s.o. RH AS 4.0). It does not appear that the computer is using > all the memory available. > > After my actual 30 arrays I must analyze 380, which problems will I face? > > Any help? > > Thanx, > > Uli > > _______________________________________________ > 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 > -- Thomas Girke, Ph.D. 1008 Noel T. Keen Hall Center for Plant Cell Biology (CEPCEB) University of California Riverside, CA 92521 E-mail: thomas.girke at ucr.edu Website: http://faculty.ucr.edu/~tgirke Ph: 951-827-2469 Fax: 951-827-4437

Hi Ulrich, If you search in the mailing list archive (http://dir.gmane.org/gmane.science.biology.informatics.conductor), you'll see a fair number of posts about this problem. You should look at the just.gcrma function instead. R tends to like making unnecessary copies of large objects, so people have recoded those functions (like gcrma) entirely in C which doesn't do that. I don't know if it'll get you all the way to your 380 arrays. Some people have suggest doing the normalization in different batches. As I said the archives should tell you more about it. Francois On Fri, 2006-06-23 at 14:53 +0200, Ulrich Pfeffer wrote: > Hi, > > when analyzing more than 25 Affymetrix HGU133plus2 arrays the analysis > fails during background correction with GCRMA and the error message says > "cannot allocate vector of 301.000kB ...." > > I got the message ot only from my PC but also form a more potent computer > (Ml570 G2, 4 CPU XEON MP 2.5/1Mb, > 16 Gb RAM, s.o. RH AS 4.0). It does not appear that the computer is using > all the memory available. > > After my actual 30 arrays I must analyze 380, which problems will I face? > > Any help? > > Thanx, > > Uli > > _______________________________________________ > 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 >