[BioC] Help using ENSMUSG ids in GOstats

Robert Gentleman rgentlem at fhcrc.org
Sun May 11 23:24:40 CEST 2008

John Reid wrote:
> Robert Gentleman wrote:
>> I am guessing you have not looked at either AnnotationDbi or 
>> AnnBuilder as packages that you can use to build an annotation package.
> I did look at AnnBuilder but the basic vignette suggested that I should 
> look in the advanced vignette for what I would like to do. I didn't find 
> the advanced vignette at that time. I shall have a look at AnnotationDbi.

   How did you not find it? It should have been included with the 
package  and so one hopes not very hard to find.  If you did look in 
specific locations you thought would contain the vignette, we would like 
to know where, so that we can try to either rectify the impression that 
something should be there, or if it is missing from some obvious places 
put it there.

>>    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.

>>   You don't tell us what organism, but I suspect that you could simply 
>> use one of the organism based annotation packages (without needing to 
>> build anything).  There are several previous threads on how to do that.
> ENSMUSG genes are mouse genes. Is there an annotation package that will 
> work for me? How could I have found it without asking here? Which 
> threads? From a wealth of packages on the annotation packages page it is 
> very hard to determine which might be relevant.

   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.


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).

  best wishes

> Thanks,
> John.
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Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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