great!!!! 100.000 not on a regular machine...

2012/2/22 Henrik Bengtsson <hb@biostat.ucsf.edu>

> 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@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@r-project.org [mailto:
> bioconductor-bounces@r-project.org] On Behalf Of Saif Ur-Rehman [guest]
> > Sent: Monday, February 20, 2012 12:09 PM
> > To: bioconductor@r-project.org; saif.urrehman@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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-- 
-----------------------------------------------------
Dr. Alberto Goldoni
Parma, Italy
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