Hi Marc,

I am trying to summarize the GO results for lots of experiments. GOslim was
recommended to me as it gives a nice overview. Ideally I would like to have
a vector for each experiment, showing a score for each GOslim term which I
can then colour/cluster based on over representation

I am not exactly sure how the process would works though.
Would I do my over representation with all GO terms, and then extract only
those that are in GOslim? Or would I have to check all GOterms that make up
each GOslim term? Just thinking about it now, if GOslim is a subset of GO
terms, I guess it makes most sense to just extract the GOslim terms from my
analysis.

Cheers,

Iain


On Thu, Feb 19, 2009 at 11:39 AM, Marc Carlson <mcarlson@fhcrc.org> wrote:

> Hi Iain,
>
> I am a little curious about what you are planning to do with GOSLIM? To
> change the annotation used in GOstats, you would normally put the name
> of the appropriate annotation package into the annotation slot of the
> GOHyperGParams object. But as I am sure you have noticed we don't have
> annotation packages for GOSLIM. However, according to the gene ontology
> website, a GOSLIM is a subset of the existing GO ontology. So the
> appropriate organism package for yeast (which is already based on what
> they have at SGD as much as possible) should already provide all the
> information you would need for that.
>
>
> Marc
>
>
>
>
> Iain Wallace wrote:
> > Hi all,
> >
> > I was wondering if somebody could point me in the right direction. I
> would
> > like to use GOSlim from the SGD
> > website<
> ftp://genome-ftp.stanford.edu/pub/yeast/data_download/literature_curation/
> >with
> > the GOStats package, but I am not sure how to change the
> > ontology/annotation.
> >
> > I am currently using the following set of commands to do my Go analysis.
> > library(GOstats)
> > library("org.Sc.sgd.db")
> > x <- org.Sc.sgdGENENAME  #To generate the set of gene names
> > mapped_genes <- mappedkeys(x)
> > sel<-mapped_genes[1:10]   #selected set of genes
> > uni<-mapped_genes           #universe of genes
> >
> params=new("GOHyperGParams",geneIds=sel,universeGeneIds=uni,annotation="org.Sc.sgd.db",ontology="BP",pvalueCutoff=0.05,conditional=FALSE,testDirection="over")
> > over=over=hyperGTest(params)
> >
> > Thanks for any help,
> >
> > Iain
> >
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> >
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> >
>
>

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