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Question: Memory issue
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gravatar for SALIL SHARMA
12.6 years ago by
SALIL SHARMA30
SALIL SHARMA30 wrote:
Hi Group, Iam a beginner in learning R and Bioconductor. I have a basic question. How can I increase the memory limit. When I type the command: abatch <- ReadAffy(filenames = myfilenames , phenoData = mypheno) It throws me this error: Error: cannot allocate vector of size 625759 Kb In addition: Warning message: Reached total allocation of 511Mb How can I overcome this? Thanks [[alternative HTML version deleted]]
ADD COMMENTlink modified 12.6 years ago by James W. MacDonald45k • written 12.6 years ago by SALIL SHARMA30
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gravatar for Wolfgang Huber
12.6 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear Salil, how much memory does your machine have? How many files are there in "myfilenames" and what chiptypes are they? You might get started with using fewer arrays; on the long run, getting more memory seems like a good idea. You can also try the justGCRMA (package gcrma) and justRMA functions: The man page says: This method should require much less RAM than the conventional method of first creating an 'AffyBatch' and then running 'gcrma'. Cheers Wolfgang Salil wrote: > Hi Group, > > Iam a beginner in learning R and Bioconductor. > > I have a basic question. > How can I increase the memory limit. > > When I type the command: > > abatch <- ReadAffy(filenames = myfilenames , phenoData = mypheno) > > It throws me this error: > > Error: cannot allocate vector of size 625759 Kb > In addition: Warning message: > Reached total allocation of 511Mb > > > How can I overcome this? > > Thanks > ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber
ADD COMMENTlink written 12.6 years ago by Wolfgang Huber13k
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gravatar for James W. MacDonald
12.6 years ago by
United States
James W. MacDonald45k wrote:
Salil wrote: > Hi Group, > > Iam a beginner in learning R and Bioconductor. > > I have a basic question. > How can I increase the memory limit. > > When I type the command: > > abatch <- ReadAffy(filenames = myfilenames , phenoData = mypheno) > > It throws me this error: > > Error: cannot allocate vector of size 625759 Kb > In addition: Warning message: > Reached total allocation of 511Mb Well, if you only have 512Mb RAM, you can overcome it by buying more. If you have more than that, you need to set your command line option --max-mem-size= to whatever amount of RAM you have. If you are on Windows, you need to set this in the Target field of your R shortcut. Jim > > > How can I overcome this? > > Thanks > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- 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
ADD COMMENTlink written 12.6 years ago by James W. MacDonald45k
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