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 However, when it comes to Kegg pathways, I tried to use go stats again but = it's based on the kegg.db which is outdated and as a result I get the follo= wing error: "Loading required package: KEGG.db Failed with error: =E2=80=98package =E2=80=98AnnotationDbi=E2=80=99 1.24.0= is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 -- Sent via the guest posting facility at bioconductor.org. _______________________________________________ Bioconductor mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatic= s.conductor