[BioC] yeast2 LOCUSID environment

John Zhang jzhang at jimmy.harvard.edu
Wed Jun 7 15:30:01 CEST 2006

>I was just wondering why there is no "LOCUSID" environment associated  
>with the yeast2 annotation package.  I know from looking up some S.  
>cerevisiae genes by hand on the Entrez Gene website that yeast genes  
>do have the Entrez accession numbers.  The lack of this environment  
>for the yeast2 package makes it difficult to use functions like  
>GOHyperG that depend on the presence of the LOCUSID environment.   
>Could someone enlighten me on this?

The yeast annotation data package uses data from the YeastGenome database. When 
the code for building the package was written, it did not appear to be a clean 
way of mapping the probes to  Entrez Gene ids. I checked the YeastGenome web 
site this morning and found that mappings between ORFs and NCBI RefSeq ids are 
available now. So, it seems to be possible to include a LOCUSID environment but 
someone has to spend a few hours to create it and make it right.   

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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084

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