[BioC] Problem with addGeneIDs and org.Sc.sgd.db

[Marc Carlson]

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
>
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