[BioC] annotation package building

[Marc Carlson]

Hi Ingrid,

Have you seen this function?

library(AnnotationForge)
?makeOrgPackageFromNCBI

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).

   Marc


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
>