[BioC] problem with Category package and custom annotationDbi

Mark Kimpel mwkimpel at gmail.com
Thu Oct 23 19:56:50 CEST 2008 

myEGs has length of 400 and all are in MyGeneUniverse, checked with
setdiff. at hospital with mother having surgery today, so will post
reproducible example when I can. assume that myEGs should be lengthy,
not sure how to post this, hence the reason I did not post already.
suggestions?

thanks Mark
------------------------------------------------------------
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 Thu, Oct 23, 2008 at 12:52 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:
> 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
>>>>
>>>>
>>>>
>>>
>>
>>
>
>

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