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
•
written
by
daniel.naumovas •
2 answers
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.
WGCNA now suggests to use anRichment::enrichmentAnalysis. Tutorial here: https://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/GeneAnnotation/Tutorials/anRichment-Tutorial1.pdf
Log in to answer this question.
-
How to launch the RnBeads graphical user interface?
written by Fede_Santos95 •
-
how to debug error in RnBeads Mac mini 10.15.7 R 4.0.3
written by saba_nasir111 •
-
RnBeads error running rnb.run.dj()
written by mario.red8976
-
dendogram in R
written by parinv •
-
WGCNA - How to get multiple clusters
written by emilaves94iv •
-
Consensus WGCNA: differentially connected genes
written by baldauf •
-
Consensus WGCNA: soft-threshold power selection
written by baldauf •
-
GOTerm enrichment rna-seq data
written by studyfranco •
-
problem in loading systemPipeR and RNASeqGene packages in R 3.4.1
written by nazaninhoseinkhan
-
Trouble with Biostrings
written by mcc
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.
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.
I am sorry, I didn't try the module you are mentioning... maybe you might ask help to the authors?
I am getting same error message. Just wait for someone to help.