[BioC] Reading 80 CEL files.

[Weiwei Shi]

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
>
>
>
>
> _____________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
>       ____________________________________________________________________________________
> Never miss a thing.  Make Yahoo your home page.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>


-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

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