Gostats Hypergeometric tests for non model organisms Kegg pathway

"Claire [guest]" <[email protected]> Tue, 9 Sep 2014 02:18:11 -0700 (PDT)
Newsgroups gmane.science.biology.informatics.conductor
Message-ID <[email protected]>
Hello

I would like to run an hypergeometric testing on KEGG terms for non-model o=
rganism. 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it's based on the kegg.db which is outdated and as a result I get the follo=
wing error:
"Loading required package: KEGG.db
Failed with error:  =E2=80=98package =E2=80=98AnnotationDbi=E2=80=99 1.24.0=
 is loaded, but >=3D 1.25.15 is required by =E2=80=98KEGG.db=E2=80=99=E2=80=
=99
In addition: Warning message:
package =E2=80=98KEGG.db=E2=80=99 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 legitima=
te KEGG IDs."

Does anyone have any recommendations for Kegg enrichment analysis for non-m=
odel organism and /or how to do an hypergeometric test with R directly?

Thanks a lot for your help

CLaire


 -- output of sessionInfo(): =


Loading required package: KEGG.db
Failed with error:  =E2=80=98package =E2=80=98AnnotationDbi=E2=80=99 1.24.0=
 is loaded, but >=3D 1.25.15 is required by =E2=80=98KEGG.db=E2=80=99=E2=80=
=99
In addition: Warning message:
package =E2=80=98KEGG.db=E2=80=99 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 legitima=
te KEGG IDs

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