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

[Robert Gentleman]

Mark,
   Category requires annotation packages, not cdfs. I am not sure why 
you think information on where a probe is located on the chip would be 
useful for a GSEA analysis, but if there is something in the docs, 
please let me know.

   You can use AnnotationDbi to build an annotation package for that 
chip, if one does not exist.  Please see the vignette etc.

   best wishes
    Robert


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.
> 
> [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
> ******************************************************************
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> 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
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org