Dear Bioconductor list, Some time ago I downloaded a Mouse annotation database from the Affymetrix web site (Version 29 according to my notes). It occasionally contains more than one gene per probeset separated by 3 slashes. For example for the probeset 1415691_at the genes listed are Dlg1 /// LOC100047603. Presumably this is because the probeset is found to have specificity for more than one gene. When I get the annotation from mouse4302.db (version 2.2.11) using the annaffy package I get only one gene per probeset for those probesets that have more than one gene in the Affy package. For example, for the case of 1415691_at it only lists Dig1. Is this because reannotation and mapping has found the gene most for which the probeset is most specific? If that is the case can you point me at a reference as to how this is done? The paper Dai et al. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res. 2005 Nov 10;33(20):e175. deals with this issue, but as best I can understand it they assign different probeset names. Or should there be multiples genes per probeset on output? Thanks and best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of Biomedical Informatics (DBMI) Educational Coordinator, Center for Computational Biology and Bioinformatics (C2B2)/ National Center for Multiscale Analysis of Genomic Networks (MAGNet) Room 824 Irving Cancer Research Center Columbia University 1130 St. Nicholas Ave New York, NY 10032 (212)851-4765 (voice) friedman at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ In Memoriam, Philip Klass

http://article.gmane.org/gmane.science.biology.informatics.conductor/2 5621/match=multiple+probeset Richard Friedman wrote: > Dear Bioconductor list, > > Some time ago I downloaded a Mouse annotation database from the > Affymetrix web site (Version 29 according to my notes). > It occasionally contains more than one gene per probeset separated by 3 > slashes. For example for the probeset > 1415691_at the genes listed are Dlg1 /// LOC100047603. Presumably this > is because the probeset is found to have > specificity for more than one gene. > > When I get the annotation from mouse4302.db (version 2.2.11) using > the annaffy package I get only one gene > per probeset for those probesets that have more than one gene in the > Affy package. For example, for the case of > 1415691_at it only lists Dig1. > > Is this because reannotation and mapping has found the gene most > for which the probeset is most specific? > If that is the case can you point me at a reference as to how this is done? > The paper Dai et al. Evolving gene/transcript definitions significantly > alter the interpretation of GeneChip data. Nucleic Acids Res. 2005 Nov > 10;33(20):e175. deals with this issue, but as best I can understand it > they assign different probeset names. > > Or should there be multiples genes per probeset on output? > > Thanks and best wishes, > Rich > ------------------------------------------------------------ > Richard A. Friedman, PhD > Associate Research Scientist, > Biomedical Informatics Shared Resource > Herbert Irving Comprehensive Cancer Center (HICCC) > Lecturer, > Department of Biomedical Informatics (DBMI) > Educational Coordinator, > Center for Computational Biology and Bioinformatics (C2B2)/ > National Center for Multiscale Analysis of Genomic Networks (MAGNet) > Room 824 > Irving Cancer Research Center > Columbia University > 1130 St. Nicholas Ave > New York, NY 10032 > (212)851-4765 (voice) > friedman at cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > In Memoriam, > Philip Klass > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab 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