On Mon, Nov 8, 2010 at 6:19 PM, Pradeep Battula <prabat@utu.fi> wrote:

> Hi, Sean.
>
>  The information provided by Steve helped me a lot in carrying out the GO
> enrichment tests. But now, I want to visualize the results in the GO graph.
> Regarding that I need suggestions.....Thank You.
>
>
Hi, Pradeep.

Sorry to be so difficult, but we cannot help you unless you try things
yourself.  Please read the help for GOgraph in the GOstats package.  If you
have problems, please send the code you tried and the error messages you
receive.

Sean



> Regards,
> Pradeep.
>
> ----- Original Message -----
> From: Sean Davis <sdavis2@mail.nih.gov>
> Date: Tuesday, November 9, 2010 1:03 am
> Subject: Re: [BioC] Need suggestions for constructing GOgraph
> To: Pradeep Battula <prabat@utu.fi>
> Cc: bioconductor@stat.math.ethz.ch
>
>
> > On Mon, Nov 8, 2010 at 5:41 PM, Pradeep Battula <prabat@utu.fi> wrote:
> >
> > > Dear BioC users,
> > >
> > > I am having the following data,
> > >
> > > background.Datat: Entrez identifiers of all probes present on Illumina
> > > human HT12 v3. microarray
> > > DEgenes.Data: Differentially expressed genes in a real study carried
> > out on
> > > Illumina HT12 v3. microarray
> > >
> > > Can anyone suggest, how to construct GOgraph for the available
> > > data....Thanks in advance.
> > >
> > >
> > Hi, Pradeep.
> >
> > You will probably want to do a hypergeometric testing procedure to
> > find the
> > enrichment of your genes in various GO categories.  I think Steve emailed
> > you how to do that a couple of days ago using the GOstats package.
> > There is
> > an mailing list archive (link attached to every email) available if you
> > missed that email.  If Steve's suggestion doesn't work for you, please
> > send
> > the code you tried, errors you received, and the output of sessionInfo().
> >
> > As for making a GO graph, you may want to take a look at the help for
> > GOgraph() in the GOstats package.  Again, if you get an error, please
> > supply
> > a reproducible example and the output of sessionInfo().
> >
> > Sean
>

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