[BioC] How can I access to a gene set

[James W. MacDonald]

Hi Lola,

Please use the 'Reply-all' button to reply, so others can see any 
helpful responses.

On 3/22/2012 10:55 AM, Lola Guerrero wrote:
>
> Hi Jim,
>
> Thanks for your proposal, as you thought I’m using GOstats package 
> (Agilent for mouse).
>
> I was trying to figure out how to use probeSetSummary function and I 
> found the following error:
>
> probeSetSummary(myhyperGTest)
>
> Error en get(mapName, envir = pkgEnv, inherits = FALSE) :
>
>   Object 'org.Mm.egENTREZID' not found
>

Yes. This means that you haven't loaded the org.Mm.eg.db package first.

Best,

Jim


> So I need to check my code and find out where the problem is. Do you 
> have any advice?
>
> Thanks,
>
> Lola.
>
>
> El 22 de marzo de 2012 a las 14:15 "James W. MacDonald" 
> <jmacdon at uw.edu> escribió:
>
> > Hi Lola,
> >
> > On 3/22/2012 8:33 AM, Lola Guerrero wrote:
> > > Dear all,
> > >
> > >
> > >
> > > I have run a Hypergeometric test and so far so good. Now I am 
> interested in the
> > > gene set that belong to a particular ontology. Do you know if 
> exist any way to
> > > access to these genes? I mean, if for example I have an ontology 
> which is
> > > defined by 10 genes and in my case the test count 5, how can I 
> access to these
> > > genes?
> >
> > It depends on what package you used. If you used the GOstats package,
> > then there is probeSetSummary().
> >
> > Best,
> >
> > Jim
> >
> >
> > >
> > >
> > >
> > > I’ll appreciate any help! Thank you very much for your help!
> > >
> > >
> > >
> > > Lola Guerrero
> > >
> > >
> > >         [[alternative HTML version deleted]]
> > >
> > >
> > >
> > > _______________________________________________
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> >
> > --
> > James W. MacDonald, M.S.
> > Biostatistician
> > University of Washington
> > Environmental and Occupational Health Sciences
> > 4225 Roosevelt Way NE, # 100
> > Seattle WA 98105-6099
> >

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099