[BioC] hg_u95av2.cdf

Laurent Gautier laurent@cbs.dtu.dk
Thu, 13 Jun 2002 10:43:43 +0200

On Thu, Jun 13, 2002 at 10:03:50AM +0200, Bart Spiessens wrote:
> I have an experiment with 5 hg_u95av2 arrays and corresponding *.CEL 
> files, which I would like to analyse with Bioconductor. Unfortunately, I 
> do not have the *.CDF file.
> 1) Does anyone know where I can get this CDF file ?

AFAIK, the manufacturer of the oligonucleotide arrays you are using is
shipping a CD-ROM along with the stuff it sold. CDF files can be found there.

Since a recent time, one can download many data files for the manufacturer's
website. This CDF file is one of them I think.

We do not distribute CDF files since we are not sure we are allowed to do so.

> if not:
> 2) I did find the file 'hg_u95av2.cdf.forR.dat' which was pre-processed 
> for use with an older version of bioconductor. Can I still use this file 
> in the new version ?

The file you mention is to be used with a package called affyR (prior to the
Bioconductor time). It is possible to convert the data formats for CDF from
affyR to affy. This is let as a (long) exercise to the reader.

> if not:
> 3) Could we reproduce the original CDF file from this forR.dat file, or 
> is there information used from the CDF file that is not in the forR.dat 
> file ?

No and yes (note: answer(first part) == not(answer(second part)), right ? ;)  )



> Thanks for any suggestions !
> Bart.
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