Hi, I'm trying to do some work on the AraGene 1_1 st plate and I have a problem with the annotation for it. If you go to the Affymetrix web page you can download the annotation for it and probe sets will be labelled with an eight digit id, e.g. 13334158. On the other hand when I read in the raw data then the CDF will label the probe sets using a more conventional Affymetrix naming convention e.g. Ara-322976_st This means we can do our analysis but it's impossible to match up the genes with the probe sets. Has anybody encountered this problem before ? Any solutions ? All the best Hugh [[alternative HTML version deleted]]

Hi Hugh, On 7/22/2013 10:58 AM, Hugh Shanahan wrote: > Hi, > I'm trying to do some work on the AraGene 1_1 st plate and I have a > problem with the annotation for it. If you go to the Affymetrix web page > you can download the annotation for it and probe sets will be labelled with > an eight digit id, e.g. 13334158. On the other hand when I read in the raw > data then the CDF will label the probe sets using a more conventional > Affymetrix naming convention e.g. Ara-322976_st This means we can do our > analysis but it's impossible to match up the genes with the probe sets. > > Has anybody encountered this problem before ? Any solutions ? It's not clear to me what you mean by 'the CDF will label the probe sets'. What CDF? Note that there isn't and hasn't been IIRC, a conventional CDF for this chip. Are you saying that the scanner returns a celfile with the wrong IDs, or is this something that is happening within a BioC package? Taking stabs in the dark, I might recommend you ensure that the scanner has the updated library file installed. I took a quick peek at the current file, and didn't see any Ara-xxxx_st probeset IDs. If the problem is due to a BioC package, please send us the code you are using and the output from sessionInfo(). Best, Jim > > All the best > Hugh > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099