I have experience with such a chip. In my experience - once you have the necessary CDF package which can be a pain - there is no problem using the standard affy functions. GCRMA however has some problems. So I guess you are doing something wrong here. Kasper On Sep 17, 2007, at 1:31 PM, lgautier at altern.org wrote: > Only to second what was stated earlier: ReadAffy has most certainly > nothing > to do with the issue. > > I have some experience with customized CDFs, but I am not certain > of what > you are doing. > > Here is the deal with CDF and CEL files: > - ReadAffy reads CEL files (and only CEL files) and builds an > AffyBatch - > The relevant CDF mapping structure (currently an R object of type > "environment") is inferred from the name for the chip type > (contained in > the header of all CEL files. That information (the name) is > available in a > slot of the AffyBatch > - The default CDF mapping structures are built from CDF files and > wrapped > into packages. > - There is a package to make the CDF packages mentioned above > ("makecdfenv"). > - The default CDF mapping structure can be changed by editing the > relevant > slot in the AffyBatch > > > Rather than painfully building a "fake" CDF file (and run into > all sort of trouble with the CDF parsers - you might not know what > consistency checks are checking), I would recommend to work on > building > directly environments (check the package altcdfenvs)... and if your > workflow requires you to have data in files, use your own simple file > format and build the R "environment" from it. > > Regarding the presence of a one probe in several probesets, I would > think that this is something you want to get rid of.. > > > Laurent > > > >> Hi, >> >> When a same probe is assigned to 2 or more probesets (in the CDF >> file), > the ReadAffy() function runs oddly. >> >> I give you an exemple to explain my problem : >> >> I create a CDF file with only 2 probesets of 11 probes (PM). In the > second >> probeset, one probe (named P) has the same coordinate than in the >> first > one. >> Then, when I read some CEL files with this cdf environment in R, the > second probeset has 11 probes but the first one has only 10 > probes : the > intensity of the probe P is missing in the first probeset. >> >> I don't understand why the function ReadAffy doesn't manage that >> type of > design ? >> Do you have any idea about this ? >> >> Best regards, >> >> Maud >> >> >> >> >> --------------------------------------------------------------------- >> -------- > AVIS : Ce courrier et ses pieces jointes sont destines a leur seul > destinataire et peuvent contenir des informations confidentielles > appartenant a bioMerieux. Si vous n'etes pas destinataire, vous etes > informe que toute lecture, divulgation, ou reproduction de ce > message et > des pieces jointes est strictement interdite. Si vous avez recu ce > message >> par erreur merci d'en prevenir l'expediteur et de le detruire, >> ainsi que > ses pieces jointes. >> >> NOTICE: This message and attachments are intended only for the use of > their addressee and may contain confidential information belonging to > bioMerieux. If you are not the intended recipient, you are hereby > notified >> that any reading, dissemination, distribution, or copying of this > message, >> or any attachment, is strictly prohibited. If you have received this > message in error, please notify the original sender immediately and > delete >> this message, along with any attachments. >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor