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")
Is there any step to do before using KEGG ?
Regards
•
written
by
Radhouane Aniba
Could you try omitting the conditional parameter. It is not valid for KEGGHyperGParams
> getClass("KEGGHyperGParams")
Class "KEGGHyperGParams" [package "Category"]
Slots:
Name: geneIds universeGeneIds annotation datPkg
Class: ANY ANY character DatPkg
Name: categorySubsetIds categoryName pvalueCutoff testDirection
Class: ANY character numeric character
Extends: "HyperGParams"
whereas it is for GOHyperGParams
> getClass("GOHyperGParams")
Class "GOHyperGParams" [package "Category"]
Slots:
Name: ontology conditional geneIds universeGeneIds
Class: character logical ANY ANY
Name: annotation datPkg categorySubsetIds categoryName
Class: character DatPkg ANY character
Name: pvalueCutoff testDirection
Class: numeric character
Extends: "HyperGParams"
Also, I would suggest to update R and Bioc to the current version, R 2.13.0 and Bioc 2.8.
Hope this help.
Absolutely laurent, look at my last comment, that's what I did actually, and it works, thanks for your answer it was useful.
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You have '+' signs in the code above. Have you run this function as it is above, or is it a copy and paste artefact?
Also, it is always helpful to post your sessionInfo() output, to inform us about the R and package versions you use.
Yes the + is copy and paste artefact
Here is the sessionInfo
R version 2.10.0 (2009-10-26) i386-pc-mingw32
Solved ! it was caused by conditional=FALSE which is not useful in case of KEGG
Oh, just saw your comment, after posting my answer.