[BioC] problem with Category package and custom annotationDbi

Mark Kimpel mwkimpel at gmail.com
Thu Oct 23 01:19:26 CEST 2008

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

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

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