[BioC] Reading 80 CEL files.

[Henrik Bengtsson]

You can also use R package aroma.affymetrix:

 http://groups.google.com/group/aroma-affymetrix/

It is cross platform and you should be able to process any number of
arrays with roughly 1-2GB of RAM.  All you need is CEL files and a CDF
file.

Cheers

Henrik

On 11/14/07, Michal Blazejczyk <michal.blazejczyk at mail.mcgill.ca> wrote:
> Hi,
>
> Yeah, typical...
>
> Try using function just.rma instead of calling ReadAffy.
> just.rma operates directly on files and requires way less
> memory.
>
> Or run it on Linux, I think there's less memory issues
> there.
>
> Good luck,
>
> Best,
> Michal Blazejczyk
> FlexArray Lead Developer
> http://genomequebec.mcgill.ca/FlexArray/
>
>
> > 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 = ¡šD://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
>
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