[BioC] topGO spurious GO terms?
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)
attached base packages:
 parallel grid stats graphics grDevices utils datasets methods base
other attached packages:
 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
 graph_1.38.3 ggplot2_0.9.3.1
loaded via a namespace (and not attached):
 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
 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
Sent via the guest posting facility at bioconductor.org.
More information about the Bioconductor