[BioC] problem with GOHyperGParams in package Category

[Mark W Kimpel]

Robert and Tony,

Deja vu all over again. I don't remember asking this before, but 
wouldn't surprise me. Need to increase my dose of Aricept I guess. That 
or stop drinking with my rats.

Yes, loading GOstats works and solved my problem. Would it not make 
sense for Category to recommend GOstats on installation and, during a 
session to load it if and when required and issue a specific warning if 
it were not found?

Mark

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

******************************************************************


Tony Chiang wrote:
> 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 at gmail.com 
> <mailto:mwkimpel at 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 at stat.math.ethz.ch <mailto:Bioconductor at stat.math.ethz.ch>
>     https://stat.ethz.ch/mailman/listinfo/bioconductor
>     Search the archives:
>     http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
>