To whom it may concern, I try to calculate Lin similarity for GO terms by SemSim package (published in 12/10/2007) and obtained some results greater than 1 since December, 2008. (e.g. termSim("GO:0045944", "GO:0007329","Lin","yeast") returns 1.232) I sent this problem to the author (xguo at jcvi.org) but the delivery was failed. After reading through the internal code, I find that the "get" function in SemSim connects to "AnnotationDbi" (published in 11/22/2008) and SemSim depends on the ".gocount" internal data which is produced before 12/10/2007. So, one of the reasons to get Lin similarity greater than 1 might be that ".gocount" did not count the common ancestors identified between 12/10/2007 and 11/22/2008. I appreciate you very much for any kind help on solving such a problem. Sincerely, Danni Yu, Ph.D. student Department of Statistics Purdue University

Hi Danni, Because we lost track of its maintainer, the SemSim package didn't make it in the current BioC release (BioC 2.3, released in last October). I can only mention 2 alternatives (maybe there are more, someone on this list will know better): (1) The GOSim package from CRAN. Not officially a BioC package but it depends heavily on other BioC packages, especially BioC annotations. (2) The GOSemSim package. Only available in BioC devel for now (so you will need R-2.9). From their Description field, these 2 packages seem to provide functionalities similar to what SemSim was doing. Cheers, H. dyu at purdue.edu wrote: > To whom it may concern, > > I try to calculate Lin similarity for GO terms by SemSim package (published in > 12/10/2007) and obtained some results greater than 1 since December, 2008. (e.g. > termSim("GO:0045944", "GO:0007329","Lin","yeast") returns 1.232) > > I sent this problem to the author (xguo at jcvi.org) but the delivery was failed. > > After reading through the internal code, I find that the "get" function in > SemSim connects to "AnnotationDbi" (published in 11/22/2008) and SemSim depends > on the ".gocount" internal data which is produced before 12/10/2007. So, one of > the reasons to get Lin similarity greater than 1 might be that ".gocount" did > not count the common ancestors identified between 12/10/2007 and 11/22/2008. > > I appreciate you very much for any kind help on solving such a problem. > > Sincerely, > > Danni Yu, > Ph.D. student > Department of Statistics > Purdue University > > _______________________________________________ > 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319