Dear Biocs, I would like to produce pie charts or similar with percentage of genes associated to selected Gene Ontologies categories (or KEGG), preferable if I can choose the categories so that I can customise them using some search by keyword option. I would like to do it to compare the percentage of genes expressed in two different samples for the selected categories. I have explored Voronto (outside Bioc) and goProfiles and GeneAnswers, but I am not sure these are the best options. Thanks in advance Regards Jose ------------------------------------------------------------ Jose M. Garcia Manteiga PhD Data analyst in Functional Genomics Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute Via Olgettina 58 20132 Milano Italy Office: +39 02 26434751

Hi Jose, On Wed, Feb 6, 2013 at 1:16 PM, Jose M Garcia Manteiga <manteiga.garcia at="" gmail.com=""> wrote: > Dear Biocs, > I would like to produce pie charts or similar with percentage of genes associated to selected Gene Ontologies categories (or KEGG), preferable if I can choose the categories so that I can customise them using some search by keyword option. > I would like to do it to compare the percentage of genes expressed in two different samples for the selected categories. > I have explored Voronto (outside Bioc) and goProfiles and GeneAnswers, but I am not sure these are the best options. So ... what's your question? :-) Are you curious how you might make such a pie chart? Or, perhaps you're not sure how to find genes associated with a given GO (or KEGG) category? or? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Hi Jose, Have you seen the GOstats package? It supports an analysis similar to what I think you are describing. You can read the vignette here: http://www.bioconductor.org/packages/2.11/bioc/vignettes/GOstats/inst/ doc/GOstatsHyperG.pdf Let me know if you have questions. Marc On 02/06/2013 10:16 AM, Jose M Garcia Manteiga wrote: > Dear Biocs, > I would like to produce pie charts or similar with percentage of genes associated to selected Gene Ontologies categories (or KEGG), preferable if I can choose the categories so that I can customise them using some search by keyword option. > I would like to do it to compare the percentage of genes expressed in two different samples for the selected categories. > I have explored Voronto (outside Bioc) and goProfiles and GeneAnswers, but I am not sure these are the best options. > Thanks in advance > Regards > Jose > > ------------------------------------------------------------ > Jose M. Garcia Manteiga PhD > > Data analyst in Functional Genomics > Center for Translational Genomics and Bioinformatics > San Raffaele Scientific Institute > Via Olgettina 58 > 20132 Milano > Italy > > Office: +39 02 26434751 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor