[BioC] annotation package building

Marc Carlson mcarlson at fhcrc.org
Tue Oct 23 19:05:36 CEST 2012

Hi Ingrid,

Have you seen this function?


It's in the AnnotationForge package.  You can use it to try and generate 
a simple organism package for your species of interest (depending on 
data availability of course).


On 10/22/2012 04:47 AM, Ingrid Mercier wrote:
> Dear list,
> I'm working on a custom chip from Roche Nimblegen, I perform to create
> an Annotation package for "pd.110916.mtub.h37rv.im.exp.til" built with
> pdInfoBuilder, and I 've identified some DEG's.
> Now I would like to do Gene Ontology and GSEA with these genes.I know I
> have to use these library(GOstats); library(GO.db); library(annotate)but
> I miss library(my_organisme.db).
> Any annotation package from my organism (Mycobacterim tuberculosis) exists .
> How can I process ? Which are suitable packages ?
> Is it the best way to do ? Can I do this with my first annotation
> package "pd.110916.mtub.h37rv.im.exp.til" ?
> Thank you for your reply,
> Cheers,
> Ingrid

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