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 Radhouane [[alternative HTML version deleted]]

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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues