thanks a lot! but when i have 2GB physical memory and 6GB of virual one, how is it possible that R runs out of memory because it can not allocate a vector of 700MB? but anyway, i will use the justRMA and everything is fine. thanks again Quoting James MacDonald <jmacdon@med.umich.edu>: > If I am not mistaken, R simply takes whatever memory is available under > linux (unlike win32 where you have the --max-memory-size flag), so if > you are running out of memory all you can do is get more. > > And yes, justRMA() does exactly the same as ReadAffy() followed by > rma(), only without an AffyBatch that can be used for certain QC plots, > etc. > > Best, > > Jim > > > > 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 >>>> "Dipl.-Ing. Johannes Rainer" <johannes.rainer@tugraz.at> 11/25/04 > 11:47 AM >>> > hi, > > i want to read in 67 CEL files (hgu133plus2 chips), but i get everytime > the > error message: "Error: cannot allocate vector of size 709203KB" > i run R (version 2.0.1, bioconductor 1.5) on a linux workstation with 2 > GB > physical RAM and 6 GB swap space... so there should not be any problem > regarding the memory installed on the system. is there a possibility to > increase the memory that can be allocated by R? > other question: the justRMA() function, does this function exactly the > same as > ReadAffy() and then rma() ? > > thanks for your help! > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should > not be used for urgent or sensitive issues. > >

Perhaps the following FAQ might be useful http://cran.r-project.org/bin/windows/base/rw-FAQ.html#There-seems-to- be-a-limit-on-the-memory-it-uses_0021 Also keep in mind that if you have already allocated 1.8 GB of memory, then requesting 0.7 GB more memory might be impossible. I am no expert in this but I would suggest to try from a fresh R session. justRMA replaces ReadAffy() + rma(). I think it is faster because it does store the intermediate affybatch object in memory. Also please search the mailing archives for similar questions and answers. Regards, Adai On Fri, 2004-11-26 at 06:57, Dipl.-Ing. Johannes Rainer wrote: > thanks a lot! > > but when i have 2GB physical memory and 6GB of virual one, how is it possible > that R runs out of memory because it can not allocate a vector of 700MB? but > anyway, i will use the justRMA and everything is fine. > > thanks again > > > Quoting James MacDonald <jmacdon@med.umich.edu>: > > > If I am not mistaken, R simply takes whatever memory is available under > > linux (unlike win32 where you have the --max-memory-size flag), so if > > you are running out of memory all you can do is get more. > > > > And yes, justRMA() does exactly the same as ReadAffy() followed by > > rma(), only without an AffyBatch that can be used for certain QC plots, > > etc. > > > > Best, > > > > Jim > > > > > > > > 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 > >>>> "Dipl.-Ing. Johannes Rainer" <johannes.rainer@tugraz.at> 11/25/04 > > 11:47 AM >>> > > hi, > > > > i want to read in 67 CEL files (hgu133plus2 chips), but i get everytime > > the > > error message: "Error: cannot allocate vector of size 709203KB" > > i run R (version 2.0.1, bioconductor 1.5) on a linux workstation with 2 > > GB > > physical RAM and 6 GB swap space... so there should not be any problem > > regarding the memory installed on the system. is there a possibility to > > increase the memory that can be allocated by R? > > other question: the justRMA() function, does this function exactly the > > same as > > ReadAffy() and then rma() ? > > > > thanks for your help! > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > ********************************************************** > > Electronic Mail is not secure, may not be read every day, and should > > not be used for urgent or sensitive issues. > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Adaikalavan Ramasamy ramasamy@cancer.org.uk Centre for Statistics in Medicine http://www.ihs.ox.ac.uk/csm/ Cancer Research UK Tel : 01865 226 677 Old Road Campus, Headington, Oxford Fax : 01865 226 962