Hello, My name is Germain and I'm Bioinformatician. I have installed R (v 2.4) on RHEL5, and I try to read 93 CEL files with ReadAffy function. Despite 8Go RAM, I obtain this error : Error: cannot allocate vector of size 762 Mo ... I read all topics about this error and try all proposed solutions, but it still doesn't work. By unix "top" command, I can seen that % of use memory keep under 20% Note that I tried with R 2.7 on the same computer but it s doesn't work too. "ulimit" command return => unlimited gc command (in R) return (before ReadAffy) > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 222874 6.0 407500 10.9 350000 9.4 Vcells 98794 0.8 786432 6.0 358096 2.8 (After ReadAffy) > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 464170 12.4 818163 21.9 597831 16.0 Vcells 215236 1.7 224490510 1712.8 280335642 2138.8 Session Info on Server with troubles > sessionInfo() R version 2.4.0 (2006-10-03) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_ MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_A DDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: affy affyio Biobase "1.12.2" "1.2.0" "1.12.2" I tried with an other server (RHEL4) with 10Go RAM and the same R version (2.4) and it's work... Session Info on Server ok > sessionInfo() R version 2.4.1 (2006-10-03) x86-64-unknow-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_ MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_A DDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: affy affyio Biobase "1.12.2" "1.2.0" "1.12.2" Any idea ? could you please help me ? THANK YOU !

See below. Germain Paimparay writes: > Sent: Wednesday, May 21, 2008 12:41 PM > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] cannot allocate vector of size 762 Mo ! One > more time ! > > > Hello, > > My name is Germain and I'm Bioinformatician. > > I have installed R (v 2.4) on RHEL5, and I try to read 93 CEL > files with ReadAffy function. > > Despite 8Go RAM, I obtain this error : > > Error: cannot allocate vector of size 762 Mo ... > > I read all topics about this error and try all proposed > solutions, but it still doesn't work. > > > By unix "top" command, I can seen that % of use memory keep under 20% > > Note that I tried with R 2.7 on the same computer but it s > doesn't work too. > > > "ulimit" command return => unlimited > > > gc command (in R) return > > (before ReadAffy) > > gc() > used (Mb) gc trigger (Mb) max used (Mb) > Ncells 222874 6.0 407500 10.9 350000 9.4 > Vcells 98794 0.8 786432 6.0 358096 2.8 > > (After ReadAffy) > > gc() > used (Mb) gc trigger (Mb) max used (Mb)Ncells 464170 12.4 818163 21.9 597831 16.0 > Vcells 215236 1.7 224490510 1712.8 280335642 2138.8 > > > > Session Info on Server with troubles > > sessionInfo() > R version 2.4.0 (2006-10-03) > i686-pc-linux-gnu > < --8<--snip---> > I tried with an other server (RHEL4) with 10Go RAM and the > same R version (2.4) and it's work... > > Session Info on Server ok > > sessionInfo() > R version 2.4.1 (2006-10-03) > x86-64-unknow-gnu < --8<--snip---> Which one of these two computers is not like the other? A 32 bit machine can only address memory (at least for a single process...such as R) up to about 4 GB because that is the limit of a 32 bit address. A 64 bit machine can address over 16 million terabytes (that would be quite a few arrays)--if only you could find a place to put all those RAM sticks. So regardless of how much memory you have, you are not going to get more than 4GB for your R session on a 32 bit processor (and maybe quite a bit less depending on the OS). Therefore, it is no wonder you had more success on the 64 bit machine. Indeed, this week I normalized 1300 hgu133plus2 CEL files via justRMA on my 64 bit server. So, as has been mentioned previously, you might try justRMA--perhaps with the destructive=TRUE option--if you need to normalize a lot of 32 bit CEL files on a 32 bit machine (avoids the call to ReadAffy). Or, do it in batches with something like mas5 and stitch the batches together. But since you apparently have access to a 64bit box, just stick to that. -Eric This email message, including any attachments, is for th...{{dropped:6}}

If your 93 CEL files are Exon arrays, then 8 GB RAM are surely not enough! Have a look at either my package "xps" available at BioC 2.2, or at package "aroma.affymetrix", both of which work with only 1 GB RAM. Regards Christian _._._._._._._._._._._._._._._._ C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._ Germain Paimparay wrote: > Hello, > > My name is Germain and I'm Bioinformatician. > > I have installed R (v 2.4) on RHEL5, and I try to read 93 CEL files > with ReadAffy function. > > Despite 8Go RAM, I obtain this error : > > Error: cannot allocate vector of size 762 Mo ... > > I read all topics about this error and try all proposed solutions, but > it still doesn't work. > > > By unix "top" command, I can seen that % of use memory keep under 20% > > Note that I tried with R 2.7 on the same computer but it s doesn't > work too. > > > "ulimit" command return => unlimited > > > gc command (in R) return > > (before ReadAffy) >> gc() > used (Mb) gc trigger (Mb) max used (Mb) > Ncells 222874 6.0 407500 10.9 350000 9.4 > Vcells 98794 0.8 786432 6.0 358096 2.8 > > (After ReadAffy) >> gc() > used (Mb) gc trigger (Mb) max used (Mb) > Ncells 464170 12.4 818163 21.9 597831 16.0 > Vcells 215236 1.7 224490510 1712.8 280335642 2138.8 > > > > Session Info on Server with troubles >> sessionInfo() > R version 2.4.0 (2006-10-03) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_ > > MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_A > > DDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "base" > > other attached packages: > affy affyio Biobase > "1.12.2" "1.2.0" "1.12.2" > > > > I tried with an other server (RHEL4) with 10Go RAM and the same R > version (2.4) and it's work... > > Session Info on Server ok >> sessionInfo() > R version 2.4.1 (2006-10-03) > x86-64-unknow-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_ > > MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_A > > DDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "base" > > other attached packages: > affy affyio Biobase > "1.12.2" "1.2.0" "1.12.2" > > > > Any idea ? could you please help me ? > > THANK YOU ! > > _______________________________________________ > 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 > >