[BioC] Gostats and custom list

[Marc Carlson]

Hi Iain,

Have you read the GOstats vignette?  It is a great place to start if you
are doing this.

It would also be great if you could have a peek at our posting guide and
then give us more details about what you are doing and what seems to
actually be going wrong???

http://www.bioconductor.org/docs/postingGuide.html

Speaking very generally, to use GOstats you need to have a list of genes
that you think are interesting.  So if you have a set of categories,
perhaps you were hoping to look at just one of the categories as
compared to all the other genes? 


  Marc




Iain Wallace wrote:
> Hi all,
>
> I was wondering if anybody could give me pointers on how to use GOstats with
> a custom list of gene annotations/categories
> I have my list of yeast genes associated with one or more of 25 different
> categories
>
> My file looks something like this:
>
> Gene_A Category_1
> Gene_A Category_2
> Gene_B Category_1
> Gene_B Category_2
> Gene_C Category_2
> Gene_C Category_3
>
> I am not sure how to convert this into an annotation that GOstats likes.
> I tried to figure out how to do it using the AnnotationDbi library, but I
> wasn't able to so any pointers would be greatly appreciated.
>
> My current GOstats command is
> params=new("GOHyperGParams",geneIds=sel,universeGeneIds=uni,annotation="org.Sc.sgd.db",ontology=class,pvalueCutoff=as.numeric(pvalue),conditional=FALSE,testDirection="over")
>     over=hyperGTest(params)
>
> Thanks,
>
> Iain
>
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