Robert, thanks for the point in the right direction. Chips I have used
previously have already had these packages built and the process has been
opaque to me. 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) 399-1219  Home
Skype:  mkimpel

"The real problem is not whether machines think but whether men do." -- B.
F. Skinner
******************************************************************


On Mon, Oct 20, 2008 at 12:48 PM, Robert Gentleman <rgentlem@fhcrc.org>wrote:

> 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@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]]
>>
>> _______________________________________________
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>>
>>
> --
> 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@fhcrc.org
>

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