[BioC] Reading 5000 celfiles with ReadAffy

[Henrik Bengtsson]

I bet a dinner w/ drinks that aroma.affymetrix can process 20,000 such
CEL files on regular machine (say >2GB of RAM).  The bet is open to
the first 3 persons who challenge me (email me).  I would be happy to
raise the number to 100,000 CEL files, but that'll be hard to find ;)

/Henrik
(author of aroma.affymetrix)

On Tue, Feb 21, 2012 at 5:49 AM, Ying Chen <Ying.Chen at imclone.com> wrote:
> Hi,
>
> You can try aroma.affymetrix, which is not a Bioconductor package yet. Or you can try the stand alone application RMAexpress as someone said he did a RMA on more than 10,000 cels with it.
>
> Ying
>
> -----Original Message-----
> From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Saif Ur-Rehman [guest]
> Sent: Monday, February 20, 2012 12:09 PM
> To: bioconductor at r-project.org; saif.urrehman at icr.ac.uk
> Subject: [BioC] Reading 5000 celfiles with ReadAffy
>
>
> 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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