On Wednesday, February 22, 2012, Henrik Bengtsson wrote:

> Hi Ying.
>
> On Wed, Feb 22, 2012 at 7:16 AM, ying chen <ying_chen@live.com<javascript:;>>
> wrote:
> > Hi Henrik,
> >
> > The regular machine does not mean windows machine, right?
>
> No, it indeed means any machine on which you can install R, e.g. OSX,
> Linux and Windows.  A good test is to see if you can install the
> affxparser package (on BioC).  If so, you can also use
> aroma.affymetrix.
>
> >  When I run aroma
> > on windows 7 64-bit machines, the problem is that the R GUI window always
> > freezes (Not Responding) when I tried to process more than 2000 cels. I
> > tried once with 1400 cels with aroma and it finished successfully :)
>
> I don't see why it should work with Rgui.  Did you make sure to
>

I don't see why it should *not* work with Rgui.

/H


> disable 'Misc -> Buffered output (Ctrl+W)' in Rgui?  That way you will
> see all messages as they appear, and not when it completed, which may
> appear as a "freeze".  If you use a high verbosity level in aroma, it
> will print lots of messages.  Also, with the buffer enabled, it may be
> that it is overflows (which then would be a bug in Rgui).  If this is
> not the cause, I'd be happy to learn more about your issues (please
> send a message to the aroma.affymetrix mailing list).
>
> FYI, I first started to develop aroma on Windows XP 32-bit w/ 1.5GB
> RAM.  Now I'm on Windows 7 64-bit w/ 8GB RAM, but the design strategy
> is still to support machines with very little RAM (~500MB) as well as
> those with lots of RAM (e.g. 128GB).  There are settings for
> specifying how much memory to occupy.
>
> [more below]
>
> >
> > Thanks,
> >
> > Ying
> >
> >> From: hb@biostat.ucsf.edu <javascript:;>
> >> Date: Tue, 21 Feb 2012 15:48:04 -0800
> >> To: Ying.Chen@imclone.com <javascript:;>
> >> CC: saif.urrehman@icr.ac.uk <javascript:;>; bioconductor@r-project.org<javascript:;>
> >> Subject: Re: [BioC] Reading 5000 celfiles with ReadAffy
> >
> >>
> >> 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 ;)
>
> Finally, since a few people emailed me offline commenting on disk
> space available on "regular" machines, the quick answer is that you'll
> need ~220GB free disk space to process 20,000 HT_HG-U133A CEL files.
> Here are the details: Each HT_HG-U133A CEL file is ~5.5Mb. 20,000 such
> CEL files occupies ~105 GB of disk space.  When running RMA, the aroma
> pipeline holds intermediate and final results on file, i.e.
> quantile-normalized data (as ~5.5Mb CEL files) and chip-effect
> estimates (as ~0.3Mb files).  Thus, for each HT_HG-U133A array
> processed, one needs ~11.5Mb of disk space. (If one is willing to
> delete the raw data one can actually get by with ~5.8Mb per array).
> Thus, to do RMA on 20,000 HT_HG-U133A CEL files, you'll need ~220GB of
> disk space.  I consider that fairly "regular" in today's standards.
> About RAM: you'll most likely will be able to get by with as little as
> 500MB of RAM.
>
> Here is what it looks like to estimate RMA chip effects (given that
> you've setup the correct aroma directory structure):
>
> # Run RMA
> ces <- doRMA("GSE24026", chipType="HT_HG-U133A");
>
> For further question about aroma.affymetrix, please head over to
> http://aroma-project.org/forum/.
>
> /Henrik
>
> >>
> >> /Henrik
> >> (author of aroma.affymetrix)
> >>
> >> On Tue, Feb 21, 2012 at 5:49 AM, Ying Chen <Ying.Chen@imclone.com<javascript:;>>
> 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 <javascript:;>
> >> > [mailto:bioconductor-bounces@r-project.org <javascript:;>] On Behalf
> Of Saif Ur-Rehman
> >> > [guest]
> >> > Sent: Monday, February 20, 2012 12:09 PM
> >> > To: bioconductor@r-project.org <javascript:;>;
> saif.urrehman@icr.ac.uk <javascript:;>
> >> > 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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> >> >
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