Hi, I'm following the chip-seq tutorial at http://evop.bioinf.uni-leipzig.de/wp- content/uploads/2012/01/chipseq_tutorial.html, and trying to do it in parallel with some actual data I have from yeast. When I try to run addGeneIDs using the org.Sc.sgd.db annotation database, I get the following: > tss_annotated_Peaks.symbol=addGeneIDs(tss_annotated_Peaks, "org.Sc.sgd.db", c("symbol", "genename")) Error: Annotation database must be *.eg.db I can't find any hits on google with anyone else trying to do this. Can anybody make any suggestions? I can see that the source for addGeneIDs does indeed require the name of the database to be *.eg.db. Is org.Sc.sgd.db simply not in a correct format, and therefore deliberately not named *.eg.db? Or is there a way to rename or alias the database so the addGeneIDs will process it? Thanks. Susan

Hi Susan, I don't think that any of us has access to "addGeneIDs()". But have you looked at the select method? You can use it with org.Hs.eg.db (for example). library(org.Hs.eg.db) ?select ## So for example if your keys were the ones stored in "k" below: k = head(keys(org.Hs.eg.db, keytype="ENTREZID")) ## Then you could do this: select(org.Hs.eg.db, keys=k, cols=c("SYMBOL","GENENAME"), keytype="ENTREZID") Marc On 08/17/2012 10:14 AM, Susan Wilson wrote: > Hi, > > I'm following the chip-seq tutorial at > http://evop.bioinf.uni-leipzig.de/wp- content/uploads/2012/01/chipseq_tutorial.html, > and trying to do it in parallel with some actual data I have from > yeast. When I try to run addGeneIDs using the org.Sc.sgd.db annotation > database, I get the following: > > > tss_annotated_Peaks.symbol=addGeneIDs(tss_annotated_Peaks, > "org.Sc.sgd.db", c("symbol", "genename")) > Error: Annotation database must be *.eg.db > > I can't find any hits on google with anyone else trying to do this. > Can anybody make any suggestions? I can see that the source for > addGeneIDs does indeed require the name of the database to be *.eg.db. > Is org.Sc.sgd.db simply not in a correct format, and therefore > deliberately not named *.eg.db? Or is there a way to rename or alias > the database so the addGeneIDs will process it? > > Thanks. > Susan > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor