[BioC] comparing GO lists

[Robert Gentleman]

Ana Conesa wrote:
> Thanks Robert for your quick response.
> 
> I was indeed trying the functions you mention from the GOstats
> packages. They requiere GO Graphs, so the question was how to
> generate a GO Graph object from a list of GOs. I was trying with the
> function makeGOgraph but again I was not able to generate the graph
> object form my list... is there a way out?

  oneGOGraph and GOGraph, again from GOstats do what I think you want, 
but let me know if you have problems with it

> I say another package on the BioC repository,SimSem, that computes
> semantic similarities (and this takes aswell gene IDs), and another
> one at CRAN GOSim - also for semantic similarity- but this gives me
> some troubles with the dependencies... So, if I can create GO graphs
> from GO lists to use the GOstats functions, I think this will be
> easiest way.

    thanks for pointing these out, I did manage to download GOsim, I am 
not sure why it is only on CRAN given that it seems to depend on a lot 
of BioC packages.
   You should be able to install it if you use install.packages, and if 
not I would contact the maintainer.

   best wishes
    Robert

> 
> regards
> Ana
> 
> 
> 
> ---- Mensaje Original ----
> De: rgentlem at fhcrc.org
> Para: aconesa at ochoa.fib.es, bioconductor at stat.math.ethz.ch
> Asunto: Re: comparing GO lists
> Fecha: Sat, 28 Jul 2007 16:15:51 -0700
> 
>> Hi Ana,
>>   I have cc'd the response to the list,
>>
>> have a look at the GOstats package (there may be others in other 
>> packages) it has simUI, simLP that take GO graphs as input. 
>> Unfortunately they do not use semantic similarity - I don't think
>> that 
>> there is anything in Bioconductor that does that (but could be
>> wrong).
>>
>> There was some software (not in R) and a paper by Peter Lord,
>> Investigating semantic similarity measures across the Gene Ontology:
>> the 
>> relationship between sequence and annotation.
>> Lord PW, Stevens RD, Brass A, Goble CA.
>> in Bioinformatics in 2003 that would be nice to have, but last time I
>>
>> looked it was not functional -
>>
>> best wishes
>>   Robert
>>
>>
>>
>>
>> Ana Conesa wrote:
>>> Hello Robert,
>>>
>>> For some reason my posting to the Bioconductor list is not working
>>> today... but I guess you are the most appropirate person for my
>>> query, so I hope you do not mind I write to you directly.
>>>
>>> Best regards,
>>>
>>> Ana
>>>
>>>
>>> Dear list,
>>>
>>> I am looking for a function to compare lists of GO terms, e.g.
>> compute
>>> semantic similarity or the minimum common graph, etc, that works
>> with
>>> GO
>>> ids... I looked into the GO packages at Bioconductor but it seems
>> to
>>> me
>>> that functions to perform such comparisons only accept as input
>> list
>>> of
>>> gene IDs, and not GO IDs. Am I right/wrong?
>>> Any help appreciated
>>>
>>> Cheers
>>>
>>> Ana
>>>
>>>
>>> ===============================================
>>> Ana Conesa, PhD
>>> Bioinformatics Department
>>> Centro de Investigacion Principe Felipe
>>> Avda Autopista Saler 16, 46013 Valencia, Spain
>>> http://bioinfo.cipf.es
>>> --------------------------------
>>> CAMDA 2007 Conference at CIPF
>>> http://camda.bioinfo.cipf.es
>>> --------------------------------
>>>
>>>
>>>
>>>
>> -- 
>> Robert Gentleman, PhD
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M2-B876
>> PO Box 19024
>> Seattle, Washington 98109-1024
>> 206-667-7700
>> rgentlem at fhcrc.org
> 
> 
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org