Question: GO enrichment analysis using R
0
gravatar for daniel.naumovas
22 months ago by
daniel.naumovas0 wrote:

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

R wgcna gene • 1.9k views
ADD COMMENTlink modified 16 months ago by Alexis Norris0 • written 22 months ago by daniel.naumovas0

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.

ADD REPLYlink written 22 months ago by Fabio Marroni2.3k

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.

ADD REPLYlink written 22 months ago by daniel.naumovas0

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

ADD REPLYlink written 22 months ago by Fabio Marroni2.3k

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

ADD REPLYlink written 22 months ago by jianxiangshi0
0
gravatar for Vitis
19 months ago by
Vitis2.2k
New York
Vitis2.2k wrote:

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.

ADD COMMENTlink written 19 months ago by Vitis2.2k
0
gravatar for Alexis Norris
16 months ago by
US/Baltimore/JohnsHopkins
Alexis Norris0 wrote:

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

ADD COMMENTlink written 16 months ago by Alexis Norris0
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