[BioC] question about GOSemSim

[James MacDonald]

-- 

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


>>> Rajarshi Guha <rajarshi.guha at gmail.com> wrote:
> Hi, does anybody know how I can get in touch ith the author of GOSemSim
> (Guangchuang Yu)? The package page nor the package contain an email address.

The package *has* to contain an email address. The Maintainer field of the DESCRIPTION file has to contain an email address or the package won't build (or check, I forget which). Anyway, from the DESCRIPTION file for GOSemSim:

Author: Guangchuang Yu
Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

Whether or not that is a real email address that the author uses is a different subject, but one would hope a package author would want to avail him/herself of user feedback.

Best,

Jim



> 
> Specially, my question regards the GO annotations of genes that come with
> the package. For example, I am currently using the annotations from
> ftp://ftp.ncbi.nih.gov/gene/DATA/ and the GO terms correspoding to a GeneID
> of 241 are  GO:0008047 and  GO:0047485.
> 
> However, if I call
> 
> geneSim('241', '2561', 'MF', 'human', 'Wang')
> 
> I get
> 
> $geneSim
> [1] 0.29
> 
> $GO1
> [1] "GO:0005488" "GO:0008047"
> 
> $GO2
> [1] "GO:0004890"
> 
> which indicates a different set of GO annotations for GeneID 241.
> 
> Does anybody know why this discrepancy might occur?
> 
> Thanks,

**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues