[BioC] help with makeGOGraph

[Marc Carlson]

Hi Clémentine,

Could you please give us your sessionInfo() and a reproducible example? 
That would allow us to be able to really find out what is happening
here.  You might want find it helpful to have a peek at the posting
guide here:

http://www.bioconductor.org/help/mailing-list/posting-guide/


  Marc



 
On 11/12/2010 07:51 AM, Clémentine Dressaire wrote:
> 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,
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> whichever ontology type I try to use:
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>     
>
> makeGOGraph(overgenes[,3],ontology="BP",removeRoot=F,mapfun=NULL,chip=ecoli2.db)
>
>                                  
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>      Erreur dans makeGOGraph(overgenes[, 3], ontology = "BP", removeRoot =
>
> F,  : 
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>      argument(s) inutilisé(s) (ontology = "BP")
>
>
>
> I wonder wether this could be due to the fact that some of the genes in
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> 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
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>