[BioC] Gostats Hypergeometric tests for non model organisms Kegg pathway

[Luo Weijun]

Claire,
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.
Details at:
http://www.bioconductor.org/packages/release/bioc/html/gage.html
http://www.bioconductor.org/packages/release/bioc/html/pathview.html


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Claire [guest] wrote: 

Hello

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However, when it comes to Kegg pathways, I tried to use go stats again but it's based on the kegg.db which is outdated and as a result I get the following error: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:  ‘package ‘AnnotationDbi’ 1.24.0 is loaded, but >= 1.25.15 is required by ‘KEGG.db’’
In addition: Warning message:
package ‘KEGG.db’ 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

CLaire