[BioC] problem with Category package and custom annotationDbi

[Mark Kimpel]

> ragene10stv1()
Quality control information for ragene10stv1:


This package has the following mappings:

ragene10stv1ACCNUM has 0 mapped keys (of 29214 keys)
ragene10stv1ALIAS2PROBE has 31410 mapped keys (of 31410 keys)
ragene10stv1CHR has 20998 mapped keys (of 29214 keys)
ragene10stv1CHRLENGTHS has 23 mapped keys (of 23 keys)
ragene10stv1CHRLOC has 13092 mapped keys (of 29214 keys)
ragene10stv1CHRLOCEND has 13092 mapped keys (of 29214 keys)
ragene10stv1ENSEMBL has 15812 mapped keys (of 29214 keys)
ragene10stv1ENSEMBL2PROBE has 14570 mapped keys (of 14570 keys)
ragene10stv1ENTREZID has 21170 mapped keys (of 29214 keys)
ragene10stv1ENZYME has 1586 mapped keys (of 29214 keys)
ragene10stv1ENZYME2PROBE has 705 mapped keys (of 705 keys)
ragene10stv1GENENAME has 21170 mapped keys (of 29214 keys)
ragene10stv1GO has 13813 mapped keys (of 29214 keys)
ragene10stv1GO2ALLPROBES has 9850 mapped keys (of 9850 keys)
ragene10stv1GO2PROBE has 7430 mapped keys (of 7430 keys)
ragene10stv1MAP has 20351 mapped keys (of 29214 keys)
ragene10stv1PATH has 4357 mapped keys (of 29214 keys)
ragene10stv1PATH2PROBE has 206 mapped keys (of 206 keys)
ragene10stv1PFAM has 17187 mapped keys (of 29214 keys)
ragene10stv1PMID has 12198 mapped keys (of 29214 keys)
ragene10stv1PMID2PROBE has 36641 mapped keys (of 36641 keys)
ragene10stv1PROSITE has 17187 mapped keys (of 29214 keys)
ragene10stv1REFSEQ has 18683 mapped keys (of 29214 keys)
ragene10stv1SYMBOL has 21170 mapped keys (of 29214 keys)
ragene10stv1UNIGENE has 17585 mapped keys (of 29214 keys)
ragene10stv1UNIPROT has 9826 mapped keys (of 29214 keys)


Additional Information about this package:

DB schema: RATCHIP_DB
DB schema version: 1.0
Organism: Rattus norvegicus
Date for NCBI data: 2008-Sep2
Date for GO data: 200808
Date for KEGG data: 2008-Sep2
Date for Golden Path data: 2006-Jun20
Date for IPI data: 2008-Sep02
Date for Ensembl data: 2008-Jul23
> sessionInfo()
R version 2.8.0 (2008-10-20)
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] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] ragene10stv1.db_1.0.0 RSQLite_0.7-0         DBI_0.2-4
[4] AnnotationDbi_1.4.0   Biobase_2.2.0         graph_1.20.0

loaded via a namespace (and not attached):
[1] cluster_1.11.11
>
------------------------------------------------------------
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 Wed, Oct 22, 2008 at 7:41 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:
> 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
>>
>> "The real problem is not whether machines think but whether men do."
>> -- B. F. Skinner
>>
>> _______________________________________________
>> 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
>>
>>
>
>