[BioC] Reading 5000 celfiles with ReadAffy

[Matthew McCall]

Saif,

You might want to consider using fRMA:
McCall MN, Bolstad BM, and Irizarry RA* (2010). Frozen Robust
Multi-Array Analysis (fRMA), Biostatistics, 11(2):242-253.
http://bioconductor.org/packages/release/bioc/html/frma.html

Best,
Matt

On Mon, Feb 20, 2012 at 12:17 PM, Paul Geeleher <paulgeeleher at gmail.com> wrote:
> 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
>
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-- 
Matthew N McCall, PhD
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