Gene ID of yeast in GOSemSim and other GO related package may need update
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Gang Chen ▴ 20
@gang-chen-3671
Last seen 6.8 years ago
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 -- Gang Chen Computer Science Ph.D Candidate Central South University, Changsha, China E-mail: chen.gang1983 at gmail.com Cell Phone:13574886823 www.gossipcoder.com
Annotation GO Yeast biomaRt GOSemSim GOSim Annotation GO Yeast biomaRt GOSemSim GOSim • 689 views
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 4.9 years ago
United States
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. http://www.bioconductor.org/docs/postingGuide.html Thanks, Marc 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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