[BioC] Error GO.db package "term is not member of any ontology"
James W. MacDonald
jmacdon at med.umich.edu
Fri Apr 9 19:18:20 CEST 2010
Hi Ana,
Ana Conesa wrote:
> Dear Jim and Vicent,
>
> Yes, I guess this is the thing. I was wondering if there was a more up-to-date
> GO.db package...
> If case you find it interesting, I found around 200 terms not present in the
> current GO.db... (see attached)
It's not particularly interesting, since it is expected. As Martin
Morgan notes in another email, this particular GO term (and likely most
if not all 200 that you found) are available in the newest version of
the GO.db package.
We have to tread a fine line between reproducibility and being
up-to-date. If we are constantly updating packages, then it is
impossible for our end users to get consistent results, as the
underlying data are constantly in a state of flux. On the other hand, if
we never update things, then we simply push data that is completely
outdated and fairly useless.
As a compromise, we update all our annotation packages every six months,
along with the release of the new version of Bioconductor. We feel this
is a good compromise between reproducibility and currentness of data. If
an end user wants to completely reproduce earlier results, she can
simply use the version of BioC that was used to generate those earlier
results. If on the other hand, she wants the most current results, those
can be obtained using the most current release.
However, as you have found, near the release date the current data
packages start to show their age (and we will be releasing the new
version of BioC in just a few weeks).
Best,
Jim
> Thanks again
>
> Ana
>
>
>
> On Friday 09 April 2010 17:19:25 James W. MacDonald wrote:
>> I think she gives the command below.
>>
>> There is a problem with the form of the call to get(); the keys are of
>> the form GO:0090153, while the key used is missing the colon. So even if
>> the term did exist in the GO.db package, it wouldn't be found using that
>> key.
>>
>> However, I think the real reason this term isn't found is that it is a
>> new term, added after the current version of the GO.db was produced.
>>
>> If you look at the term information on the AmiGO website, the source is
>> stated to be ascb_2009. Since the GO.db package is now 6 months out of
>> date, I wouldn't be surprised if this term were added after we built
>> this package last.
>>
>> Best,
>>
>> Jim
>>
>> Vincent Carey wrote:
>>> What is the exact command you are running that generates the error?
>>> Present it in a way that another person not using your computer can
>>> generate it.
>>>
>>> On Fri, Apr 9, 2010 at 9:17 AM, Ana Conesa <aconesa at cipf.es> wrote:
>>>> Thanks Sean for your fast reply
>>>>
>>>> This is my sessionInfo()
>>>>
>>>>> sessionInfo()
>>>> R version 2.10.0 (2009-10-26)
>>>> x86_64-pc-linux-gnu
>>>>
>>>> locale:
>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>>> [11] 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_2.3.5 RSQLite_0.7-1 DBI_0.2-4
>>>> [4] annotate_1.24.1 AnnotationDbi_1.8.2 Biobase_2.6.1
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] xtable_1.5-5
>>>>
>>>>> get('GO0090153',GOTERM)
>>>> Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :
>>>> value for "GO0090153" not found
>>>>
>>>> Any hint?
>>>>
>>>> Ana
>>>>
>>>> On Friday 09 April 2010 15:03:20 Sean Davis wrote:
>>>>> get('GO0090153',GOTERM)
>>>> --
>>>> Ana Conesa
>>>> Bioinformatics and Genomics Department
>>>> Centro de Investigaciones Principe Felipe
>>>> Avda. Autopista Saler 16,
>>>> 46012 Valencia, Spain
>>>> Phone: +34 96 328 96 80
>>>> Fax: +34 96 328 97 01
>>>> http://bioinfo.cipf.es/aconesa
>>>> http://www.blast2go.org
>>>> ==========================================
>>>> FIRST INTERNATIONAL COURSE IN AUTOMATED
>>>> FUNCTIONAL ANNOTATION AND DATA MINING
>>>> Valencia/Orlando, September/October 2009
>>>> http://bioinfo.cipf.es/blast2gocourse
>>>>
>>>> _______________________________________________
>>>> 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
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> 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
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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
--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
More information about the Bioconductor
mailing list