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 ? 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 ? 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 ? Thanks for any suggestions ! Bart.

also, who ever gave you the cel files must have affymetrix's MAS. if you use find on that computer you should be able to find the file. rafael On Thu, 13 Jun 2002, 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 ? > 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 ? > 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 ? > > Thanks for any suggestions ! > Bart. > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

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 ? ;) ) regards, Laurent > Thanks for any suggestions ! > Bart. > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- other email: lgautier@altern.org -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student D-2800 Lyngby,Denmark tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent

Bart, > 1) Does anyone know where I can get this CDF file ? Just ask Affymetrix support in the UK or US by phone - they are usually happy to send out the cdf files. Make sure that they compress the file and that your email account can handle emails of approx. 6 MB size - otherwise your email admin might go nuts when their 30MB file hits your mailbox. Gerry Jacobsen Contentsoft AG http://www.contentsoft.de GeneViz - Free academic version downloadable now