Hi, Ana,

The most current version is 2.4.1 (which is what Sean Davis used to
fetch the GO:0090153 information).  Installing the dev-R (2.11.0) will
allow you to install and use this newer version of GO.db.  Once you
install R2.11.0, start R and enter

    source("http://bioconductor.org/biocLite.R")
    biocLite("GO.db")

The source code can be found here:
http://www.bioconductor.org/packages/2.6/data/annotation/html/GO.db.html

I check the first 5 term on your list, they are not GO terms. At least I
cannot find them in AmiGo. Are you sure those "GO" terms really exist?

Chao-Jen

On 04/09/10 08:30, 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)
>  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@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@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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>
>
>   
>
>
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-- 
Chao-Jen Wong
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., M1-B514
PO Box 19024
Seattle, WA 98109
206.667.4485
cwon2@fhcrc.org


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