[BioC] increase memory size in R, problem reading 67 affy CEL
ramasamy at cancer.org.uk
Fri Nov 26 13:12:32 CET 2004
Perhaps the following FAQ might be useful
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
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 at 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 at 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!
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Adaikalavan Ramasamy ramasamy at 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
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