Entering edit mode
Last seen 2 days ago
Hi George, Please don't take list conversations off-list. The list archives are intended to be a source of information, and on the off chance that I might say something useful, it would be nice if people could find this later. As to your question, as I said below, we just map things from Entrez Gene to the other annotation sources, so whatever Entrez Gene says, we report. So if I grep out some probeset ID that maps to multiple UniGene IDs, I might get something like 35566_f_at, which maps to 5 UG IDs. Now if I get the Entrez ID (3576), go to the Entrez Gene webpage for this ID, and scroll to the very bottom, I see five UniGene IDs that this Entrez Gene ID corresponds to. We report four of these five, the only difference being we report Hs.443948 instead of Hs.654584. This is obviously a mistake because Hs.443948 is SLC4A1 instead of IL-8, but the hgu95av2 package was built on March 15, so maybe Entrez Gene has corrected this mistake in the interim. See http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dop t=full_report&list_uids=3576 Best, Jim Tseng, George C. wrote: > Jim, > > Thanks so much for your response. I have one further question. In > your annotation in Bioconductor, a probe set can map to multiple > unigene ID. This really confuses me. Shouldn't it be only one ID? > > George > > -----Original Message----- From: James MacDonald > [mailto:jmacdon at med.umich.edu] Sent: Sunday, April 01, 2007 9:59 AM > To: Tseng, George C. Cc: biocannotation at lists.fhcrc.org; Lu, Shu- Ya > Subject: Re: Annotation of U95av2 array > > Hi George, > > Tseng, George C. wrote: > >> Dear Dr. MacDonald and other Biocore Data Team members, >> >> I'm using your array annotations from Bioconductor in my research >> and I teach it in my microarray course as well. It is indeed a >> great tool for our data analysis and methodological development. >> Recently we're working on a meta-analysis research project to >> incorporate information from multiple data sets. My student took >> the Unigene ID annotations in all the U95av2 probes and compared >> with the result obtained from the Affymetrix website (the batch >> search in NetAffy). Among the 9704 probes annotated in >> Bioconductor, 724 probes were annotated completely differently in >> NetAffy. >> >> My question is: Do you obtain your Unigene ID annotation from >> Affymetrix database or other source? NetAffy annotations always >> have one Unigene ID to a probeset while your annotationis can have >> many. Can you give us some detail about your annotation procedure? > > > Nianhua Li makes the annotation packages, so she would be the final > trusted source. > > In the past, the process was to map Affy ID to Entrez Gene ID using > the annotation files that Affy supply on their website. We then use > AnnBuilder to do the mappings from Entrez Gene to all other > annotation sources, so it is not inconceivable that we would have > different UniGene IDs for a given probeset. > > In my experience, the BioC annotations are more up to date and > accurate than what Affy supply either on Netaffx or in their > annotation files. This is based on blatting the probe sequences. > > Best, > > Jim > > > >> Thanks! >> >> George >> >> ============================================ George C. Tseng >> Assistant Professor Dept of Biostatistics and Human Genetics, >> University of Pittsburgh http://www.pitt.edu/~ctseng, >> 412-624-5318 ============================================ > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.