[BioC] Reading 5000 celfiles with ReadAffy

[Ying Chen]

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

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