[BioC] GOstats Annotation Package

"Jörg Linde" Edd17 at gmx.de
Fri Mar 13 13:33:26 CET 2009

Dear Joern,

I am sorry for the late reply. I just wanted to thank you for your advise. It was extremely helpful.  The package "topGo" is exactly what I was looking for.

Thank you so much

-------- Original-Nachricht --------
> Datum: Wed, 25 Feb 2009 16:07:53 +0000
> Von: Joern Toedling <toedling at ebi.ac.uk>
> An: "Jörg Linde" <Edd17 at gmx.de>
> CC: bioconductor at stat.math.ethz.ch
> Betreff: Re: [BioC] GOstats Annotation Package

> Hello,
> there are functions in the AnnotationDbi package for building custom
> ".db" annotation packages. See the vignette "SQLForge" in that package
> for details. This functionality is meant to supersede the AnnBuilder
> package, which could be used to generate annotation package of the
> previous generation.
> The package topGO allows for such a test without requiring an annotation
> package. Similar to the conditional hypergeometric test, topGO also
> includes variants of the hypergeometric test that take the structure of
> the GO into account. See the paper by Alexa et al. (2006) for details:
> http://bioinformatics.oxfordjournals.org/cgi/content/full/22/13/1600
> Regards,
> Joern
> Jörg Linde wrote:
> > Hello,
> > is there any way to build an annotation package usable with GOstats on
> your own??? I don't have any Microarray data but I still want to use Gostats
> to look for overrepresented terms in some gene lists. I would like to
> build an annotation package using the annotations from GO homepage directly. 
> > Is there any way?
> > I know this is possible with topGO but there is no conditional
> hypergeometric test, is it?
> >
> > Thanks for your answer!
> > Jörg 
> > --
> >   

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