[BioC] topGO spurious GO terms?

Adam [guest] guest at bioconductor.org
Tue Dec 17 14:35:49 CET 2013

I am using topGO's custom workflow to get enrichment of GO terms. In my top 20 nodes there are significant GO terms that are not found in my "universe". I am new to analyzing GO information and I can only assume that these spurious GO IDs are part of pathways of GO IDs in my universe and are significant by association? Alternatively, topGO has a more updated list of GO IDs and has substituted the names in my universe. Any advice would be greatly appreciated!

 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] parallel  grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] topGO_2.12.0         SparseM_1.03         GO.db_2.9.0          RSQLite_0.11.4       DBI_0.2-7            AnnotationDbi_1.22.6 Biobase_2.20.1       BiocGenerics_0.6.0  
 [9] graph_1.38.3         ggplot2_0.9.3.1     

loaded via a namespace (and not attached):
 [1] colorspace_1.2-4   dichromat_2.0-0    digest_0.6.3       gtable_0.1.2       IRanges_1.18.4     labeling_0.2       lattice_0.20-24    MASS_7.3-29        munsell_0.4.2     
[10] plyr_1.8           proto_0.3-10       RColorBrewer_1.0-5 reshape2_1.2.2     scales_0.2.3       stats4_3.0.1       stringr_0.6.2      tools_3.0.1       

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