[BioC] Reading 5000 celfiles with ReadAffy

[cstrato]

To reply to Henrik's challenge.
As Paul mentioned xps is able to process this amount of CEL-files. In 
fact quite some time ago a user of xps was able to process 23,000 
CEL-files of HG-U133_Plus_2 arrays. As far as I remember memory usage 
was about 2-2.5 GB RAM.

Christian
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C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
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On 2/22/12 12:48 AM, Henrik Bengtsson wrote:
> 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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