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 -- Ingrid MERCIER Mycobacterial Interactions with Host Cells Team Institute of Pharmacology& Structural Biology CNRS BP 64182 F-31077 Toulouse Cedex France Tel +33 (0)5 61 17 54 63 [[alternative HTML version deleted]]

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 >