[BioC] problem with Category package and custom annotationDbi

[Marc Carlson]

Hi Mark,

If the package you built and installed were called "MarkPackage.db",
then what would be the output of "MarkPackage()" (right after you loaded
it)?  Also, what is the output of sessionInfo()?

  Marc




Mark Kimpel wrote:
> Today I believe I successfuly built a annotation package for my Affy
> Rat Gene ST data using annotationDbi, at least I got no errors during
> the build and it loads properly. I get the following error output,
> however, when I try to run hyperGTest, package Category, on a vector
> of Entrez Gene IDs and a vector of the gene universe of the chip. I
> suspect I did something wrong when building the annotation package,
> but I have no clue what that could be. I've used this same code with
> chipsets whose annotation packages are built by the BioConductor team
> without issue.
>
>   
>> params <- new("GOHyperGParams", geneIds = myEGs,
>>     
> +                   universeGeneIds = myGeneUniverse,
> +               annotation = annotation(AOP$eSet),
> +                   ontology = "BP", pvalueCutoff = 0.05, conditional
> = TRUE, testDirection = "over")
>   
>> params
>>     
> A GOHyperGParams instance
>   category: GO
> annotation: ragene10stv1
>   
>> hyperGTest(params)
>>     
> Error in getUniverseHelper(probes, datPkg, entrezIds) :
>   No Entrez Gene ids left in universe
>
> Enter a frame number, or 0 to exit
>
> 1: hyperGTest(params)
> 2: .valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase", "hyperGT
> 3: is(object, Cl)
> 4: is(object, Cl)
> 5: universeBuilder(p)
> 6: universeBuilder(p)
> 7: getUniverseViaGo(p)
> 8: getUniverseHelper(probes, datPkg, entrezIds)
>
> Selection: 8
> Called from: eval(expr, envir, enclos)
> Browse[1]> ls()
> [1] "datPkg"    "entrezIds" "probes"    "univ"
> Browse[1]> datPkg
> An object of class "ArabadopsisDatPkg"
> Slot "name":
> [1] "ragene10stv1"
>
> Browse[1]> entrezIds[1:5]
> [1] "65049"  "60444"  "313914" "140941" "306868"
> Browse[1]> probes[1:5]
> [1] "10701636" "10701643" "10701654" "10701663" "10701679"
> Browse[1]> univ
> character(0)
> Browse[1]>
>
> ------------------------------------------------------------
> 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
>
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> -- B. F. Skinner
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