[BioC] help with makeGOGraph

[Clémentine Dressaire]

Dear BioC users,



I am trying to construct a GOgraph using a gene list (overgenes[,3]) of

messengers that I previously identified as overexpressed in the condition I

was interested in. I previoulsy used this same gene list to perform

hypergeometric tests and it worked well. 



With makeGOgraph I systematically get the following error message,

whichever ontology type I try to use:

    

makeGOGraph(overgenes[,3],ontology="BP",removeRoot=F,mapfun=NULL,chip=ecoli2.db)

                                 

     Erreur dans makeGOGraph(overgenes[, 3], ontology = "BP", removeRoot =

F,  : 

     argument(s) inutilisé(s) (ontology = "BP")



I wonder wether this could be due to the fact that some of the genes in

the list do not have GO annotation...(then does it mean that I have to

eliminate them? If so what would be the simplest way?)



Does anyone can throw light on this issue for me?



Many thanks for your help,



Clémentine





-- 

Clémentine Dressaire

Post-doctoral research fellow

Control of gene expression lab

ITQB - Instituto de Tecnologia Química e Biológica

Apartado 127, Av. da República

2780-157 Oeiras

Portugal

+351 214469562