comparing GO lists
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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 7.4 years ago
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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
Annotation GO Cancer graph GOstats Annotation GO Cancer graph GOstats • 1.1k views
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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 7.4 years ago
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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
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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
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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 7.4 years ago
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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
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Ana Conesa ▴ 130
@ana-conesa-2246
Last seen 8.1 years ago
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
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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
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Ana Conesa ▴ 130
@ana-conesa-2246
Last seen 8.1 years ago
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
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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
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Hi Ana, Robert, Robert Gentleman wrote: > > 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. In this case, it will be easier if you use biocLite. I just tried it with from R-2.5.1 and R-devel and it worked fine: > source("http://bioconductor.org/biocLite.R") > biocLite("GOsim") ... it can take a while ... > library(GOSim) > sessionInfo() R version 2.5.1 (2007-06-27) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY =en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELE PHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: GOSim mclust cluster GOstats Category Matrix "1.0.2" "3.1-1" "1.11.7" "2.2.6" "2.2.3" "0.999375-0" lattice genefilter survival KEGG RBGL annotate "0.15-11" "1.14.1" "2.32" "1.16.1" "1.12.0" "1.14.1" Biobase GO graph "1.14.0" "1.16.0" "1.14.2" biocLite "knows" where to pickup the dependencies and it will choose the Bioconductor pkgs that correspond to _your_ version of R. Cheers, H. > > best wishes > Robert >
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Ana Conesa ▴ 130
@ana-conesa-2246
Last seen 8.1 years ago
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
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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
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