[BioC] increase memory size in R, problem reading 67 affy CEL files

[Adaikalavan Ramasamy]

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 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