Gostats : Kegghypergparams Error

Question

[Radhouane Aniba]

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

[Laurent]

You have '+' signs in the code above. Have you run this function as it is above, or is it a copy and paste artefact?

[Laurent]

Also, it is always helpful to post your sessionInfo() output, to inform us about the R and package versions you use.

[Radhouane Aniba]

Yes the + is copy and paste artefact

[Radhouane Aniba]

Here is the sessionInfo

R version 2.10.0 (2009-10-26) i386-pc-mingw32

[Radhouane Aniba]

Solved ! it was caused by conditional=FALSE which is not useful in case of KEGG

[Laurent]

Oh, just saw your comment, after posting my answer.

Answer 1

[Laurent]

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.

[Radhouane Aniba]

Absolutely laurent, look at my last comment, that's what I did actually, and it works, thanks for your answer it was useful.