increase memory size in R, problem reading 67 affy CEL files
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@james-w-macdonald-5106
Last seen 19 minutes ago
United States
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.
Microarray Cancer Microarray Cancer • 738 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 19 minutes ago
United States
R is not complaining that it cannot allocate a total of 700Mb, but that it ran out of memory at a point where it was trying to allocate 700Mb to a certain task. 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> 11/26/04 1:57 AM >>> 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. > > ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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