[BioC] SemSim returns Lin similiarity greater than 1 (01-06-2009).

Hervé Pagès hpages at fhcrc.org
Wed Jan 7 00:58:55 CET 2009

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.


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
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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