[BioC] Problem with hyperGTest using ath1121501.db

[Ulrike Goebel]

Thanks a lot, Marc -- it works now !

Ulrike

mcarlson at fhcrc.org schrieb:
> Hi Ulrike,
>
> Thanks for pointing this out.  I have just updated this package for 
> you.  Please try out the ath1121501.db_2.2.12.tar.gz version and let 
> me know if you have any other problems with it.
>
>
>   Marc
>
>
>
>
> Quoting Ulrike Goebel <ugoebel at mpiz-koeln.mpg.de>:
>
>> Dear list,
>>
>> I seem to have a problem with an obsolote GO id in  ath1121501.db.
>>
>>> paramsCondOver <- new("GOHyperGParams", geneIds=H3K27me3_BP,
>> universeGeneIds=uBP, annotation="ath1121501.db", ontology="BP",
>> pvalueCutoff=hgCutoff, conditional=TRUE, testDirection="over") ;
>>> hgCondOver <- hyperGTest(paramsCondOver) ;
>>> summary(hgCondOver)
>> Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :
>> value for "GO:0006118" not found       The GO database release
>> 2009-05-10 says "This term was made obsolete because it describes a
>> molecular function." Having realized this, I removed all gene ids from
>> both H3K27me3_BP and  uBP that had this term as sole annotation. But
>> the error persists. (This is the only case where I had a problem with
>> ath1121501.db's new capability of using AGIs -- normally it works fine
>> !)
>>
>> H3K27me3_BP and uBP consist of Arabidopsis Genome Initiative (AGI)
>> identifiers. The lists are too long to post, but I could send them if
>> needed.
>>
>>> sessionInfo()
>> R version 2.9.0 (2009-04-17)
>> 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] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] GO.db_2.2.11         ath1121501.db_2.2.11 GOstats_2.10.0
>> [4] RSQLite_0.7-1        DBI_0.2-4            graph_1.22.2
>> [7] Category_2.10.0      AnnotationDbi_1.6.0  Biobase_2.4.1
>>
>> loaded via a namespace (and not attached):
>> [1] annotate_1.22.0   genefilter_1.24.0 GSEABase_1.6.0    RBGL_1.20.0
>> [5] splines_2.9.0     survival_2.35-4   tools_2.9.0       XML_2.3-0
>> [9] xtable_1.5-5
>>
>>
>>
>>
>>
>> -- 
>>  Dr. Ulrike Goebel
>>  Bioinformatics Support
>>  Max-Planck Institute for Plant Breeding Research
>>  Carl-von-Linne Weg 10
>>  50829 Cologne
>>  Germany
>>  +49(0) 221 5062 121
>>
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>
>
>


-- 
  Dr. Ulrike Goebel
  Bioinformatics Support
  Max-Planck Institute for Plant Breeding Research
  Carl-von-Linne Weg 10
  50829 Cologne
  Germany
  +49(0) 221 5062 121