[BioC] GOstats : KEGGHyperGParams error

[James W. MacDonald]

Hi Radhouane,

On 5/6/2011 1:55 PM, Radhouane Aniba wrote:
> Hello,
>
> I have a bug with GOstats when I'm trying to use KEGGHyperGParams, here is
> the error message
>
> Error in .nextMethod(.Object = .Object, ...) :
>    invalid names for slots of class "KEGGHyperGParams": conditional
>
> I used it the same way I used GOHyperGParams
>
> Here is my code
>
>> param<- new("KEGGHyperGParams", geneIds=selected,
> +              annotation="org.Gg.eg.db", pvalueCutoff=0.1,
> +              conditional=FALSE, testDirection="over")

It's not a bug - there is no conditional argument for KEGG.

The conditional argument for GO attempts to account for the DAG 
structure of GO wherein any given term includes all of the more specific 
(offspring) terms. If some of the offspring terms are already 
significant, then you wouldn't want to add them into the ancestor term 
as well, because you would be 'cheating' by double counting already 
significant terms.

KEGG doesn't have this DAG structure, so a conditional argument is 
nonsensical (and hence, doesn't exist).

Best,

Jim


>
> Is there any step to do before using KEGG ?
>
> Regards
>
> Radhouane
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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