[BioC] affy & problems with memory

[Benjamin Otto]

I forgot: If concerning GCRMA and RMA you could use justGCRMA and justRMA
which are less memory consuming...

regards,
Benjamin

>
>
> 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
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
>
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