[BioC] comparing GO lists

[Ana Conesa]

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?
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.

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