[BioC] problem with Category package and custom annotationDbi

[Robert Gentleman]

Hi Mark,

   Please, you have posted often enough here and on the R list to know 
to follow the posting guide.  You will need to post a reproducible 
example as well as the things that you already provided (like 
sessionInfo) and you should not really need us to be asking you to do 
that, at this point.  In my experience, spending the few minutes it 
takes to create a reproducible example for others to use is sufficient 
to help you find the error.

   My guess is that either your list of EG ids (myEGs) is very short, 
and hence has no matches in the universe (also I have no idea what the 
universe is: myGeneUniverse) and perhaps there is no overlap, or the 
universe is remarkably small - in which case you would certainly get 
this answer.  In this case the error is not likely to be with how you 
constructed the package do note (from your later email)

ragene10stv1GO has 13813 mapped keys (of 29214 keys)

  so only about 47% of your keys have any GO annotation - again, you 
could easily check to see if the genes in myEGs have annotations.

  best wishes
    Robert



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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-- 
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