Question: Visualising the GO structure (RNA-seq) using topGO, and goseq
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gravatar for Paolo Sonego
8.7 years ago by
Paolo Sonego140
Italy
Paolo Sonego140 wrote:
Dear Marc, Thanks for the answer! I'll take a look at the suggested vignette (I read it long ago and I forgot Occam's razor) and see if I can adapt the described procedure to my pipeline. Regards, Paolo Message: 17 Date: Tue, 29 Mar 2011 16:53:05 -0700 From: Marc Carlson <mcarlson@fhcrc.org> To: bioconductor@r-project.org Subject: Re: [BioC] Visualising the GO structure (RNA-seq) using topGO and goseq Message- ID: <4D9270E1.1000303@fhcrc.org> Content-Type: text/plain Hi Paolo, Not quite sure what you want from your post, but you might want to have a look at the vignette titled " Visualizing Data Using GOstats" in the GOstats package. It shows many ways to use GO.db and how to visualize the structure of the gene ontologies. You can see it here: http://www.bioconductor.org/help/bioc- views/devel/bioc/html/GOstats.html Marc On 03/28/2011 03:12 AM, Paolo Sonego wrote: > > Hi all, > > I'd like to investigate how signi�cant GO terms are distributed over the GO > > graph for RNA-seq differentially expressed genes checked for > > over-reppresentation using the procedure available in the goseq package. The > > topGO package (see, for example, the chapter 7.4 of the included vignette) > > allows this kind of visualization for microarray data. > > Any idea how this kind of visualization can be produced for RNAseq data > > inspected using goseq? > > > > Any idea would be appreciated! > > > > Regards, > > Paolo > > > > [[alternative HTML version deleted]] > > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives:http://news.gmane.org/gmane.science.biology.i nformatics.conductor [[alternative HTML version deleted]]
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