[BioC] Reading 80 CEL files.

Weiwei Shi helprhelp at gmail.com
Sun Nov 18 06:06:14 CET 2007


Oscar,

I am curious how long it runs and the configuration of the linux cluster.


weiwei

On 11/17/07, olsen <olsen2002 at yahoo.com> wrote:
>
> >
> > Hello~~~
> >
> >
> >
> > I am trying to read 80 HG-U133A arrays so I did as
> > follows:
> >
> >
> >
> > > memory.limit(size=4095)
> >
> > > options(object.size=10000000000, digits=8,
> > scipen=100, memory=3200483647,
> > contrasts=c("contr.treatment", "contr.poly"))
> >
> > > library(affy)
> >
> > > cel.file <- ReadAffy(celfile.path = ¡¨D://CEL)
> >
> >
> >
> > However, it showed
> >
> >
> >
> > Error: cannot allocate vector of size 309.4 Mb
> >
> >
> >
> > I have tried adding the --max-mem-size=2Gb tag onto
> > my shortcut.
> >
> > The machine has 2G RAM and a 3.30GHz processor.
> >
> > Is there any idea to let R use more memory anywhere?
> >
> > Thank you~
> >
> >
> >
> > Best Regards,
> >
> > Pure
> >
> Pure,
>
> My advice: run them in Linux. We have run up to 1000
> arrays in a linux cluster.
>
> Oscar Puig
>
>
>
>
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-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
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