Hi Mark,

Paul Shannon asked the very same question a while back I think. The Category
package will work to do the testing for KEGG, but you will also have to load
the GOstats package for the testing in GO. Trying also loading this package
and see if you problem is solved or still persists. Either way, let me know.

Cheers,
--Tony

On Thu, Mar 6, 2008 at 5:41 AM, Mark W Kimpel <mwkimpel@gmail.com> wrote:

> Tonight I set about to generalize a function I had written to do GO
> analysis using the package GOstats, and to do this by switching to
> package Category. I wanted to add KEGG testing to the GO testing I have
> been doing. All I did to my code was to add a conditional such that if
> the category was KEGG a KEGGHyperGParams object would be created, else
> if it was BP, MF, or CC a GOHyperGParams object would be created. Then
> the object params would be tested. I did not change my GOHyperGParams
> generating code and, curiously, the KEGG option works beautifully.
> However, whenever I use a GO category I get a strange error message (see
> below for this and sessionInfo. I seem to remember something odd like
> this happening when some objects with the same name collided, but I'm
> not sure how that could be happening.
>
> Output is below, help is appreciated.
>
> Mark
>
> ######################
> #my code: CatToTest is either "KEGG", "BP, "MF, or "CC".
>
> if (CatToTest == "KEGG"){
>   params <- new("KEGGHyperGParams", geneIds = selectedEntrezIds,
>               universeGeneIds = entrez.universe.vec,
>                annotation = annotationPckg,
>               pvalueCutoff = hgCutoff, testDirection = testDirection)
> } else {
>   params <- new("GOHyperGParams", geneIds = selectedEntrezIds,
>               universeGeneIds = entrez.universe.vec,
>               annotation =  annotationPckg,
>               ontology = CatToTest, pvalueCutoff = hgCutoff,
>               conditional = TRUE, testDirection = testDirection)
> }
>
> test.obj<-hyperGTest(params)
> ######################################
> # error out
> GO.out <- Cat.anal.func(CatToTest = Cats[i],
> Error in getClass(Class, where = topenv(parent.frame())) :
>   c("\"GOHyperGResult\" is not a defined class", "\"BPHyperGResult\" is
> not a defined class")
>
> Enter a frame number, or 0 to exit
>
>  1: Cat.anal.func(CatToTest = Cats[i], input.df = pcmt1.cor.nodes,
> annotationPc
>  2: CatHyperMaxCats.func(CatToTest, optimizedParam)
>  3: hyperGTest(params)
>  4: .valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase",
> "hyperGT
>  5: is(object, Cl)
>  6: .class1(object)
>  7: .class1(object)
>  8: .hyperGTestInternal(p)
>  9: new(className, pvalues = stats$p[ord], oddsRatios =
> stats$odds[ord], expect
> 10: getClass(Class, where = topenv(parent.frame()))
> ############################################################
> #sessionInfo()
> R version 2.6.1 (2007-11-26)
> x86_64-unknown-linux-gnu
>
> locale:
>
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
>  [1] tcltk     splines   tools     stats     graphics  grDevices datasets
>  [8] utils     methods   base
>
> other attached packages:
>  [1] GO.db_2.0.2         rat2302_2.0.1       qvalue_1.12.0
>  [4] Category_2.4.0      genefilter_1.16.0   survival_2.34
>  [7] annotate_1.16.1     xtable_1.5-2        AnnotationDbi_1.0.6
> [10] RSQLite_0.6-8       DBI_0.2-4           graph_1.16.1
> [13] Biobase_1.16.3
>
> loaded via a namespace (and not attached):
> [1] cluster_1.11.10 RBGL_1.14.0
>
>
>
> --
>
> Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
>
> 15032 Hunter Court, Westfield, IN  46074
>
> (317) 490-5129 Work, & Mobile & VoiceMail
> (317) 204-4202 Home (no voice mail please)
>
> mwkimpel<at>gmail<dot>com
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

