We have developed a new meta-analysis system for GEO database at http://seq.mc.vanderbilt.edu/exalt/ Welcome any comments and suggestions. Yajun Yi

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

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

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