How to compare GO results
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@johannes-hanson-3621
Last seen 6.6 years ago
Dear Alex and other list members, The suggested script works nicely. However I get another problem when I using two specific lists of genes. The lists compare fine with all other lists but not with each other. I get the error only when I use onto='CC' or 'BP', but not 'MF'. Suggestions are most welcome. My code: >library(goProfiles) >library(org.At.tair.db) >L2Plus26=compareGeneLists(MyList2,MyList6, level=2, orgPackage='org.At.tair.db', onto='CC') Error in ancestors[[i]] : subscript out of bounds > sessionInfo() R version 2.10.0 Under development (unstable) (2009-05-22 r48594) i386-apple-darwin8.11.1 locale: [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] org.At.tair.db_2.3.4 goProfiles_1.7.0 GO.db_2.3.0 RSQLite_0.7-2 DBI_0.2-4 AnnotationDbi_1.7.11 Biobase_2.5.6 loaded via a namespace (and not attached): [1] tools_2.10.0 On 19 Aug 2009, at 20:32, Alex Sanchez wrote: > Hello > > goProfiles works with 'organism' anotation packages ('org.XXX.XXX.db') > There is an Arabidopsis annotation package 'org.At.tair.db' in the > next version of BioC althoug I'm not sure if this is the one you need. > You will find it in the Bioc-development site. > http://www.bioconductor.org/packages/2.5/data/annotation/html/org.At .tair.db.html > > Once you have installed it the use with goProfiles should be > straightforward. > > For instance > > library(goProfiles) > library(org.At.tair.db) > tab1 <- toTable(org.At.tairENTREZID) > genes <- sample(tab1[,1],100) > ara.MF.Profiles <-basicProfile(genelist=genes, onto='MF', level=2, > orgPackage="org.At.tair.db", empty.cats=FALSE) > print(ara.MF.Profiles) > > will yield a basic profile at level 2 of the MF ontology for a > random sample of 100 Arabidopsis genes > > I have tried it with R-2.10.0 but it should work with R-2.9.z > > Alex > > -------------------------------------------------------------------- --------------------------------- > > Dr. Alex S?nchez. > Associate professor. Statistics Department. University of Barcelona. > Facultat de Biologia UB. Avda Diagonal 645. 08028 Barcelona. Spain > asanchez_at_ub.edu > Statistics and Bioinformatics Unit > Institut de Recerca. Hospital Universitari Vall 'Hebron > Passeig Vall d'Hebron 112-119. 08034 Barcelona > asanchez_at_ir.vhebron.net > -------------------------------------------------------------------- -------------------------------- > > > > > > > ----- Original Message ----- From: "Johannes Hanson" > <s.j.hanson at="" uu.nl=""> > To: "Alex Sanchez" <asanchez at="" ub.edu=""> > Sent: Wednesday, August 19, 2009 11:25 AM > Subject: Re: [BioC] How to compare GO results > > > Thanks, THis software is answering most of the questions I have - > excellent. > > However I am working with Arabidopsis data (Affymetrix ATH1 slides). > As far as I understand the annotations files are not availible for > arabidopsis. Is that something that can be solved no or in the future > releases. > > Johannes > > On 15 Sep 2009, at 10:03, Alex Sanchez wrote: > >> Hi Johannes >> >> There are several packages in BioC that you can use to do GO >> analysis or to mine GO analysis results. >> You can find most, if not all, of them in the Bioconductor GO task >> view. (Curiously topGO is not there). >> >> http://www.bioconductor.org/packages/release/GO.html >> >> I am the maintainer of the 'goProfiles' package which is, in >> principle, developed to answer the type of question you pose. >> If you have any questions about its use I'll be pleased to try to >> help you at answering them. >> >> best >> >> Alex S?nchez >> >> ................................................................... ............................................ >> Dr. Alex S?nchez. >> Associate Professor. Statistics Department. University of Barcelona. >> Facultat de Biologia UB. Avda Diagonal 645. 08028 Barcelona. Spain >> asanchez_at_ub.edu >> Statistics and Bioinformatics Unit >> Institut de Recerca. Hospital Universitari Vall 'Hebron >> Passeig Vall d'Hebron 112-119. 08034 Barcelona >> asanchez_at_ir.vhebron.net >> ................................................................... ............................................ >> >> >> >> >> >> >>> Message: 17 >>> Date: Wed, 12 Aug 2009 09:10:56 +0200 >>> From: Johannes Hanson <s.j.hanson at="" uu.nl=""> >>> Subject: [BioC] How to compare GO results >>> To: bioconductor at stat.math.ethz.ch >>> Message-ID: <02C00589-9261-449C-B8A4-D7C8C4986E72 at uu.nl> >>> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes >>> >>> Dear all, >>> >>> This might not be a specific BioConductor question. However, >>> BioConductor is my major tool and therefore I ask the question here. >>> If not appropriate please ignore. >>> >>> I am analyzing array data from a set of mutants all showing the same >>> phenotype. The idea was of course to find genes similarly >>> expressed in >>> all mutants to get closer to the regulatory mechanism of the >>> phenotype. >>> Surprisingly there was nearly no overlap among the differentially >>> expressed genes. The suggestion was raised that the genes might >>> encode >>> similar functions. I therefore conducted GO analysis (using topGO >>> and >>> other packages). Still very little obvious overlap but how to >>> quantify >>> it? How to determine the degree of similarity between different GO >>> results? >>> >>> All suggestions are welcome. >>> >>> Johannes Hanson >>> Molecular Plant Physiology, Utrecht University >>> >>> >> > >
Annotation GO topGO goProfiles Annotation GO topGO goProfiles • 580 views
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