[BioC] Help using ENSMUSG ids in GOstats

John Reid j.reid at mail.cryst.bbk.ac.uk
Mon May 12 09:45:00 CEST 2008

Robert Gentleman wrote:
>>>    I am also guessing you have not searched the email list archives 
>>> for any of the several previous discussions (that is a good place to 
>>> start).
>> I did search the email list archives. Nothing came up. Can you 
>> suggest a good search term?
>   GOstats seems like a good starting place.  Again, you seem not to 
> want to say what you did search on, so I have no idea why nothing came 
> up. The question has been asked quite a few times.
I did search on GOstats, that certainly didn't help me find an 
annotation package. All the GOstats documentation says is that I need an 
annotation package. It does not help the user determine how to find the 
correct one. I'm not saying it should, just that this information is not 
easy to find anywhere else either.
>   Given that you have mouse genes, then I think you might be able to 
> rule out most of the annotation packages. The BioC views let you 
> select an organism, which greatly reduces the set you would need to 
> look at.
> I get to this place with about 3 clicks from the top of the BioC page.
> http://www.bioconductor.org/packages/release/Mus_musculus.html
> And then since you don't have an array it seems unlikely that any of 
> the array specific packages would be what you want.  I hope with a few 
> minutes work you would have ended up at org.Mm.eg.db, which you may be 
> able to adapt to your needs.  You may need some other tool (such as 
> biomaRt) to map from what ever identifiers you are using to those in 
> the annotation package (or they might be there already, again you 
> haven't given us much of anything to work with).

I don't understand why you keep saying I haven't given you much to work 
with. The question surely is: Are ENSMUSG identifiers mapped in an 
annotation package so that I can use them in GOstats? This seemed clear 
to me in the first list post. Perhaps I have misunderstood some of the 
issues but at the moment I don't see what. Maybe you could enlighten me?

I did end up at org.Mm.eg.Db myself also in a few clicks but it 
certainly doesn't use Ensembl identifiers, its description clearly 
states Entrez genes. So like you say I have extra work to do to map the 

Thanks for the help,

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