[BioC] Yeast annotations

Marc Carlson mcarlson at fhcrc.org
Wed Mar 5 18:00:34 CET 2008

Devarajan, Karthik wrote:
> Hi Mark,
> I was using the gene identifiers from the SGD - they look like S000001,
> S000002 etc. I have now been able to map these to corresponding yeast
> ids and it's working!
> Thanks very much for your help with this. 
> Do you know when org.Sc.sgd.db will be supported?
> Best,
> Karthik
Hi Karthik,

I am glad to hear that you found out what the problem was and that
everything is working now.

As for your question about the org.Sc.sgd.db, I can't know for sure
because you never posted enough of an example for me to replicate
everything that you were doing.  But in the email you sent to me before
you had this:

> params <- new("GOHyperGParams", geneIds=gene.id,
universeGeneIds=gene.all, annotation="org.SC.sgd.db", ontology="CC",
pvalueCutoff=hgCutoff,conditional=FALSE, testDirection="over")

> hgOver <- hyperGTest(params)

Error: getAnnMap: package org.SC.sgd not available

And THAT will definitely not work just because the actual package is
called "org.Sc.sgd.db" and not "org.SC.sgd.db"...  The "org.Sc.sgd.db"
package should have everything in it that you would find in the "YEAST"
package.  So I would be surprised if that package does not work for you
here as well.


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