[BioC] Reading 5000 celfiles with ReadAffy

[Paul Geeleher]

Hi Saif,

The R packages "XPS"
(http://www.bioconductor.org/packages/release/bioc/html/xps.html) or
"Aroma affy" (http://www.aroma-project.org/) should be able to
normalize such a massive datasets without loading it into memory.

Paul.

On Mon, Feb 20, 2012 at 5:09 PM, Saif Ur-Rehman [guest]
<guest at bioconductor.org> wrote:
>
> Hi,
>
> A student in my institute is trying to normalise >5000 celfiles generated on the U133A platform using the affy BioConductor library.
>
>
>
> Attempting to read in this many files results in an error in allocating the matrix which is as follows.
>
> allocMatrix: too many elements specified.
>
> As there is plenty of memory allocated to R this was surprising.
>
> Some Googling showed that there is a hard limit of +2,147,483,647 in the no. of columns in a matrix  specified by C  which leads to this error.
>
> I was just writing to ask if anyone had experience with normalisation of a large no. of celfiles and had encountered this problem and if so what if any solution you found?
>
> Thank you in advance.
>
> Sincerely,
> Saif Ur-Rehman
>
>  -- output of sessionInfo():
>
> NA
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
Paul Geeleher (PhD Student)
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com