[BioC] Gostats Hypergeometric tests for non model organisms Kegg pathway
luo_weijun at yahoo.com
Wed Sep 10 00:29:29 CEST 2014
You can try GAGE/Pathview for non-model organisms. They support ~3000 KEGG species. However, you need to have the full dataset instead of a pre-selected list of differentially expressed genes.
Claire [guest] wrote:
I would like to run an hypergeometric testing on KEGG terms for non-model organism. When it comes to Goterm I always use Gostats where I can enter my "universe" list and then my "target" genes and it works really well.
However, when it comes to Kegg pathways, I tried to use go stats again but it's based on the kegg.db which is outdated and as a result I get the following error:
"Loading required package: KEGG.db
Failed with error: â€˜package â€˜AnnotationDbiâ€™ 1.24.0 is loaded, but >= 1.25.15 is required by â€˜KEGG.dbâ€™â€™
In addition: Warning message:
package â€˜KEGG.dbâ€™ was built under R version 3.1.0
Error in .testKEGGFrame(x, organism) :
None of elements in the 1st column of your data.frame object are legitimate KEGG IDs."
Does anyone have any recommendations for Kegg enrichment analysis for non-model organism and /or how to do an hypergeometric test with R directly?
Thanks a lot for your help
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