Dear all,
actually i have also the same problem,
my server runs since last thursday trying to make a cdf package. currently i
use the affymetrix ExACT software to normalize the exon data. as far as i
have seen the ExACT scripts are perl scripts which compile and run smoothly
in unix (we had problems running the precompiled versions on windows, so i
compiled them from the source in linux).
so currently i use ExACT for the normalization (quantile) and summarization
(RMA, using just the PM) and analyze the normalized data in R

best, jo

On 4/8/06, Michael Seewald <mseewald@gmail.com> wrote:
>
> Dear all,
>
> Is it possible to analyze Affymetrix exon arrays with R/Bioconductor? I
> tried to generate a cdf environment with makecdfenv (as suggested by
> James),
> however the command never finished. The R process grows until it takes
> about
> 8 GB of RAM, then it is stuck.
>
> I am grateful for any help or advice.
>
> Best wishes,
> Michael
>
>
>
> On 11/23/05, James W. MacDonald <jmacdon@med.umich.edu> wrote:
> >
> > Natalia Becker wrote:
> > > I have just started working with the GeneChip(r) Human Exon 1.0 ST
> Array
> > (
> > > v2 release version of the library files) from Affymetrix.
>
> >
> > >  Unfortunately the R package "affy" doesn't accept the .CLF and .PGF
> > files.
> > >
> > > Could you send me the HuEx-1_0-st-v2.cdf file or show me the way how I
> > can
> > > create the CDF file by my own?
> >
> > You can use make.cdf.package() or make.cdf.env() in the makecdfenv
> > package.
> >
> > Best,
> > Jim
> >
>
> --
> Dr. Michael Seewald
> Bioinformatics
> Bayer HealthCare AG
>
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>
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--
Johannes Rainer, Msc
Tyrolean Cancer Research Institute
Innrain 66, 6020 Innsbruck, Austria
Tel.: +43 512 570485 15
Email: johannes.rainer@tcri.at
          johannes.rainer@tugraz.at

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