[BioC] comparing GO lists
rgentlem at fhcrc.org
Sun Jul 29 05:26:23 CEST 2007
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.
> ---- 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
>> there is anything in Bioconductor that does that (but could be
>> There was some software (not in R) and a paper by Peter Lord,
>> Investigating semantic similarity measures across the Gene Ontology:
>> 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
>> 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,
>>> Dear list,
>>> I am looking for a function to compare lists of GO terms, e.g.
>>> semantic similarity or the minimum common graph, etc, that works
>>> ids... I looked into the GO packages at Bioconductor but it seems
>>> that functions to perform such comparisons only accept as input
>>> gene IDs, and not GO IDs. Am I right/wrong?
>>> Any help appreciated
>>> Ana Conesa, PhD
>>> Bioinformatics Department
>>> Centro de Investigacion Principe Felipe
>>> Avda Autopista Saler 16, 46013 Valencia, Spain
>>> CAMDA 2007 Conference at CIPF
>> 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
>> 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
rgentlem at fhcrc.org
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