[BioC] help with using Category package with makecdfenv built Gene ST package

[James W. MacDonald]

Mark Kimpel wrote:
> I have built a package with makecdf using files supplied by Affy for their
> Rat Gene ST array. It does not seem to work with the Category package as it
> does not seem to have GO information incorporated. Output with some
> debugging info is below. Far below is the script I used to generate the Gene
> ST package.

I would certainly hope a package built with makecdfenv would be devoid 
of GO information.

Best,

Jim


> 
> [1] "beginning Category analysis"
> Loading required package: ragene10stv1.cdf.db
> Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
>   variable "ragene10stv1.cdfGO" was not found
> 
> Enter a frame number, or 0 to exit
> 
>  1: limma.contrast.output.func(AOP, fit2, rslt, contrast.num = 1,
> custom.contra
>  2: category.wrapper.func(CatToTest = "ALL", FC.dir = "all", input.df =
> t.tab.a
>  3: Cat.anal.func(CatToTest[i], input.df, FC.dir, annotationPckg,
> entrez.univer
>  4: CatHyperMaxCats.func(CatToTest, optimizedParam)
>  5: hyperGTest(params)
>  6: .valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase",
> "hyperGT
>  7: is(object, Cl)
>  8: is(object, Cl)
>  9: universeBuilder(p)
> 10: universeBuilder(p)
> 11: getUniverseViaGo(p)
> 12: eapply(ID2GO(datPkg), function(goids) {
> 13: ID2GO(datPkg)
> 14: ID2GO(datPkg)
> 15: getAnnMap("GO", p at name)
> 16: get(mapName, envir = pkgEnv, inherits = FALSE)
> 17: get(mapName, envir = pkgEnv, inherits = FALSE)
> 
> Selection: 17
> Called from: eval(expr, envir, enclos)
> Browse[1]> ls()
> [1] "envir"    "inherits" "mode"     "pos"      "x"
> Browse[1]> ls(envir)
> [1] "i2xy"             "ragene10stv1.cdf" "ragene10stv1.dim" "xy2i"
> 
> 
> Browse[1]> sessionInfo()
> R version 2.8.0 beta (2008-10-10 r46685)
> 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=C;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 utils
>  [8] datasets  methods   base
> 
> other attached packages:
>  [1] ragene10stv1.cdf_1.19.0 qvalue_1.15.0           affycoretools_1.13.4
>  [4] annaffy_1.13.1          KEGG.db_2.2.5           gcrma_2.13.2
>  [7] matchprobes_1.13.1      biomaRt_1.15.4          GOstats_2.7.0
> [10] Category_2.7.6          genefilter_1.21.5       survival_2.34-1
> [13] RBGL_1.17.2             annotate_1.19.3         xtable_1.5-4
> [16] GO.db_2.2.5             AnnotationDbi_1.3.12    RSQLite_0.7-0
> [19] DBI_0.2-4               limma_2.15.16           affy_1.19.4
> [22] preprocessCore_1.3.4    affyio_1.9.1            Biobase_2.1.7
> [25] graph_1.19.6
> 
> loaded via a namespace (and not attached):
> [1] cluster_1.11.11 GSEABase_1.3.6  RCurl_0.91-0    XML_1.98-0
> 
> 
> require(makecdfenv)
> setwd('~/R.functions/Annotation_builds/Rat_ST_1.0_lib_files')
> 
> system('mv RaGene-1_0-st-v1.r3.cdf RaGene-1_0-st-v1.cdf')
> 
> cdf.file <- "RaGene-1_0-st-v1.cdf"
> pckg.name <- substring(cleancdfname(cdf.file), 1,
> nchar(cleancdfname(cdf.file)) - 4, unlink = TRUE)
> make.cdf.package(cdf.file, species = "Rattus_nor", packagename=pckg.name)
> 
> #followed by R CMD INSTALL of package
> ------------------------------------------------------------
> 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) 399-1219  Home
> Skype:  mkimpel
> 
> "The real problem is not whether machines think but whether men do." -- B.
> F. Skinner
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662