Hi all, 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? Thanks, Jake

>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. >Thanks, > >Jake > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084