[BioC] affy & problems with memory

[Benjamin Otto]

Hi Nick,

I'm currently working on that chip type myself on a system with 512MB RAM
and had to increase the memory assigned to R too. However
"--max-mem-size=1024Mb" seems to be ok in my case. Besides the problem of
how much memory is necessary for the hgu133plus2 maybe somebody out there
could answer me this two related questions:
* I'm running R under WinXp AND under Linux on the same machine. However
there has never been any memory problem in linux. So is the memory
allocation or the  assignment of the max. memory size that can be used by R
different in the two systems?
* With my 512MB RAM system the old maximum memory value under WinXP was
512MB. Is this just a coincidence or does this maximum value rise to 1024MB
if I upgrade my system to 1024MB RAM?

regards,
Benjamin

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of James W.
> MacDonald
> Sent: 10 January 2006 20:02
> To: Ettinger, Nicholas
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] affy & problems with memory
>
>
> Ettinger, Nicholas wrote:
> > Hello all!
> >
> > I have 16 Affy Hg-U133plus2 cel files that I am trying to analyze.  I am
> > having difficulties generating expression data because of memory
> > problems.  I am working on a Dell desktop running WinXP.  I can
> > successfully generate expression values if I use "RMA" but if I try MAS5
> > or GCRMA or LiWong instead then I consistently get an error message with
> > "Cannot allocate vector of size 169362 Kb."  To try to increase
> > available memory I have already done two things:  (a) I right-clicked on
> > the R icon and changed the box labeled 'Target' to read "C:\Program
> > Files\R\R-2.2.0\bin\Rgui.exe" --sdi  --max-mem-size=2000M" and (b) I
> > have increased the virtual memory Total Page File size to 2000MB.  But
> > it still runs out of memory.
> >
> > Help! Any suggestions -- I don't really have access to any bigger
> > computers?
>
> You don't need a bigger computer, you need more RAM, which is pretty
> cheap these days. I can't imagine it would take more than 512 Mb to do
> 16 U133 plus 2 chips, so you might look into adding a 512 Mb stick.
>
> Best,
>
> Jim
>
>
> >
> > Thanks.
> > ---Nick
> >
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> > Bioconductor at 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
>
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