[BioC] problem with Category package and custom annotationDbi

Thu Oct 23 18:52:04 CEST 2008

Hi Mark,

>From that output it looks like your package was made successfully.  I
suspect that if you show us an example of what you were doing that we
might find the trouble in there.

  Marc

Mark Kimpel wrote:
>> 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
>>>
>>>
>>>       
>>     
>
>