[BioC] Gene ID of yeast in GOSemSim and other GO related package may need update

Marc Carlson mcarlson at fhcrc.org
Thu Sep 10 21:54:47 CEST 2009

Hi Gang,

Could you please give me the results of you sessionInfo() as well as
enough information (code and IDs used etc.) to reproduce the trouble
that you are experiencing?  Also, it's possible that you might find it
helpful to review out posting guide.




Gang Chen wrote:
> Hi All,
> I met a problem when I try to use GOSemSim and GOSim to calculate the
> GO semantic similarities between yeast proteins. Both of the two
> packages work well on other organisms.
> I use biomaRt package to map the Swiss Acc name to NCBI gene ID.
> Unfortunately, when I use GOSemSim and GOSim package to calculate the
> semantic similarity between genes, both of the two packages told me
> that none of these genes has GO annotation. I check this manually and
> found that nearly all yeast genes in NCBI database have been updated
> at 6th, September. Therefore, I think related annotation packages in
> Bioconductor need update to solve this problem.
> I wonder if there is any other way to solve this problem? Any comments
> or advice are welcome.
> Thanks the developers of these packages.
> Gang Chen

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