[BioC] Need suggestions for constructing GOgraph

[Pradeep Battula]

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.

Regards,
Pradeep.

----- Original Message -----
From: Sean Davis <sdavis2 at mail.nih.gov>
Date: Tuesday, November 9, 2010 1:03 am
Subject: Re: [BioC] Need suggestions for constructing GOgraph
To: Pradeep Battula <prabat at utu.fi>
Cc: bioconductor at stat.math.ethz.ch


> On Mon, Nov 8, 2010 at 5:41 PM, Pradeep Battula <prabat at 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