Hi, I have 10 marker probe sets identified using Affy CDF (Hg 133A array). How can I find the corresponding probe set ID in the data normalized with MNBI entrez CDF file? Thanks, -James [[alternative HTML version deleted]]

Hi James it seems that nobody has answered your question because it is too vague. What exactly do you mean by "corresponding"? Once you figure that out, it should also become clearer how to do it. Best wishes Wolfgang James Anderson: > Hi, > > I have 10 marker probe sets identified using Affy CDF (Hg 133A array). How can I find the corresponding probe set ID in the data normalized with MNBI entrez CDF file? > > Thanks, > > -James > > > > [[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 -- Best wishes Wolfgang -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber/contact

Hello, I missed this email previously, but I have an answer (I guess). First of all, the MBNI Custom CDF is a new annotation of the Affymetrix CDF, so the number of probes in a probeset might be different. Additionally, some genes that were present on Affy might be gone with the MBNI Custom CDF and vice versa. Nevertheless, if you want to find corresponding probesetIDs, I guess it is best to consider the probe packages: extract the probe sequences from the affy CDF and match them with the MBNI CDF. The matches give you one (or more!) probeset IDs / probeset. Manual verification / curation of the probeset assignments is required I guess. Regards, Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: Philip.deGroot at wur.nl <mailto:philip.degroot at="" wur.nl=""> Internet: http://www.nutrigenomicsconsortium.nl <http: www.nutrigenomicsconsortium.nl=""/> http://humannutrition.wur.nl <http: humannutrition.wur.nl=""/> https://madmax.bioinformatics.nl <https: madmax.bioinformatics.nl=""/> ________________________________ From: Wolfgang Huber [mailto:whuber@embl.de] Sent: Tue 6-4-2010 22:41 To: James Anderson Cc: bioconductor Subject: Re: [BioC] how to find the probe set ID using different CDF file? Hi James it seems that nobody has answered your question because it is too vague. What exactly do you mean by "corresponding"? Once you figure that out, it should also become clearer how to do it. Best wishes Wolfgang James Anderson: > Hi, > > I have 10 marker probe sets identified using Affy CDF (Hg 133A array). How can I find the corresponding probe set ID in the data normalized with MNBI entrez CDF file? > > Thanks, > > -James > > > > [[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 -- Best wishes Wolfgang -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber/contact