GO enrichment analysis using R

Question

[daniel.naumovas]

Hey, I am new to R, but already have successfully used WGCNA package to get interesting modules. Problem is when I try to perform GO enrichment analysis I am always getting same error :

Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object 'Ontology' not found

Could somebody help?

P.S. When I work with WGCNA and R I do step by step tutorial "Tutorial for the WGCNA package for R" by Peter Langfelder and Steve Horvath.

Thank You -DN

[Fabio Marroni]

Can you post the command resulting in the error, and the page and file of the tutorial you are using? I performed some analysis using the tutorial and never had problems, but maybe I didn't try the module you are trying.

[daniel.naumovas]

Tutorial page: https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/ PDF: https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/Simulated-07-Membership.pdf I am getting error after doing step 4b.

[Fabio Marroni]

I am sorry, I didn't try the module you are mentioning... maybe you might ask help to the authors?

[jianxiangshi]

I am getting same error message. Just wait for someone to help.

Answer 1

[Vitis]

I saw the same problem with the tutorial. I suspect the problem is with the "AnnotationDbi" package, or its incompatibility with WGCNA. I think the error message is saying there is no object or class called "Ontology" by AnnotationDbi. Indeed, this is true, there is no Ontology class in AnnotationDbi, only GOterm class, but for some reason, WGCNA is still trying to call Ontology from AnnotationDbi. However, I'm not using the most recent R and WGCNA. Maybe I'll try a clean R, that might fix the incompatibility here.

Answer 2

[Alexis Norris]

WGCNA now suggests to use anRichment::enrichmentAnalysis. Tutorial here: https://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/GeneAnnotation/Tutorials/anRichment-Tutorial1.pdf