[BioC] GOstats Annotation Package

[Joern Toedling]

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 
> --
>