Hello, thanks Jim for your reply. The org.Mm.eg.db::org.Mm.egSYMBOL has the gene symbol for the probeset of interest, it's just mouse4302 that's missing it. I've just checked in an older netffx annotation files (older than 2007, 2009, and the current one from 2010). The probeset was annotated already in 2007, but it was always assigned to two Entrez Gene Ids: 100047700 /// 13094, the 2nd one seems to be the correct Id and the first one was removed from entrez gene Oct 28th 2010 (flagged "withdrawn"). Note that the first Id is the withdrawn one ... If the bioc annotation pipeline comes across ambiguous annotation, that it cannot resolve, does it ignore the annotation (since there is no unique gene Id available), and therefore sets the entrez gene id to NA? Note, the gene id in entrez gene was flagged "withdrawn" in October this year, and the date of the Entrez used in mouse4032 is September 2010 (i.e. the entry was still valid in entrez gene - and therefore ambiguous ...). I'm asking because I found I found this gene interesting form some reason and it was annotated as Cyp2b9 in our gene expressino software (using netaffx) but not annotated at all in one of my post-processing pipelines that uses the mouse4302.db from bioc. kind regards, Arne ps: the probeset I'm talking about is 1419590_at "James W. MacDonald" 12/20/2010 09:58 PM To arne.mueller@novartis.com cc bioconductor@stat.math.ethz.ch Subject Re: [BioC] affymetrix annotation Hi Arne, On 12/20/2010 11:26 AM, arne.mueller@novartis.com wrote: > Hello, > > I was wondering where the mapping from affy probeset Ids to genes > (EntrezGene) is coming from (package mouse4302.db). > mouse4302.db::mouse4302_dbInfo lists all data sources (URLs) However, > what's the "original" link between an affy probeset and an EnterzGene Id, > is it Netaffx? My problem is that I've an "interesting" probeset that is > annotated with an EntrezGene in Netaffx but the mouse4302SYMBOL map > contains NA for this probeset Id. > > I'd be happy if someone could point me to some documentation how this > annotation/mapping is derived or let me know what I'm doing wrong ...? I doubt you are doing anything wrong. This may have changed a bit from the last time I talked to Marc, but in the past we needed a 'primary' mapping to start with, and chose the Affymetrix probeset ID --> Entrez Gene mapping that you can get from the latest Affy annotation file. We assumed this to be the truth, and then did all the other mappings from Entrez Gene. The problem with this is that we are by definition using more dated information than you will typically get from Netaffx. So it is quite likely, given the fluid nature of this field, that some probesets will have different data in Netaffx than what you can get from the annotation packages. As an aside, does this probeset have an Entrez Gene ID in the annotation package? Best, Jim > > thanks a lot for your help, > > arne > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues [[alternative HTML version deleted]]