[BioC] Problem with hyperGTest using ath1121501.db -- oops - another one !

[Ulrike Goebel]

Hi Marc,

well, now I get
 > summary(hgCondUnder)
Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :
  value for "GO:0044085" not found

with the same lists and test direction "under". Strange, because this GO 
term does exist !

Regards, Ulrike

Ulrike Goebel schrieb:
> 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