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

[Marc Carlson]

Hi Ulrike,

I have also tracked down this problem (which was different) and
eliminated it as well.  Thank you for letting me know about it!  You
should move on to the 2.2.13 version of the ath1121501.db package at
this time.  Please let me know if you have any other troubles after
upgrading.


  Marc



Ulrike Goebel wrote:
> 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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>>>
>>>
>>>
>>
>>
>
>