Thank you Adrian, following the instructions, I got it to work! Another question, can you provide a rough calculation of the memory usage of a topGOdata object, given the number of GO terms and genes? Thanks, -JJ -- JJ Chai National Center for Computational Sciences Computer Science and Mathematics Div Oak Ridge National Laboratory On Thu, Jan 16, 2014 at 11:41 AM, Adrian Alexa <adrian.alexa@gmail.com>wrote: > Hi JJ, > > yes, you should be able to do that with topGO. Please read through Section > 4.3 in the package vignette on how to use custom annotations: > > http://www.bioconductor.org/packages/release/bioc/vignettes/topGO/in st/doc/topGO.pdf > > You can't specify a level and chose to test only the GO terms on that > level. That won't be much useful and it won't really take advantage of the > GO hierarchy. > > Hope this helps. > > > Regards, > Adrian Alexa > > > > > > On Wed, Jan 15, 2014 at 10:40 PM, JJ [guest] <guest@bioconductor.org>wrote: > >> >> I have annotated some genomes with my own protein function annotation >> pipeline. Each genome will have a list of genes and their corresponding GO >> terms. In my annotation, the GO terms are on all kinds of different levels >> because of the hierarchical structure of GO itself. >> >> So my input will be all the GO terms for one (or a few) genome of >> interest, and a bigger set of background GO terms. I would like to figure >> out which GO terms are enriched in the interesting genomes and what they do. >> >> It'll be great if I could also specify on what level the GO terms are >> summarized. >> >> Can topGO handle this kind of problem? If not, any suggestions? >> >> Thanks a lot! >> >> -JJ >> >> >> >> >> >> -- output of sessionInfo(): >> >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] grid parallel stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] AnnotationForge_1.4.4 org.Hs.eg.db_2.10.1 GOFunction_1.10.0 >> Rgraphviz_2.6.0 >> [5] ALL_1.4.16 topGO_2.14.0 SparseM_1.03 >> GO.db_2.10.1 >> [9] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.24.0 >> Biobase_2.22.0 >> [13] BiocGenerics_0.8.0 graph_1.40.1 BiocInstaller_1.12.0 >> >> loaded via a namespace (and not attached): >> [1] IRanges_1.20.6 lattice_0.20-24 stats4_3.0.2 tools_3.0.2 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]