[BioC] Error GO.db package "term is not member of any ontology"

[James W. MacDonald]

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 Since the GO.db package is now 6 months out of 
date, I wouldn't be surprised if this term were added after we built 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
>>
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-- 
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
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