Hi everyone
I will be brief
How can I choose the hub genes in a Signed coex network? I have seen Many posts here, and I have found:
(A) choosing kME over 0.75: I have My own list with kME of My modules
(B) Using cytoscape cytohubba: For me, did not work in the 3.8 version of cytoscape
(C) Using a command from WCGNA: chooseTopHubInEachModule, But I think it choose just 1 gene.
I think I'm a little bit lost, would be great if anyone could help me to clarify this and give me your experience choosing hub genes.
Thank you so much!
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ovariohisterectomia •
You can quite easily edit the WGCNA function so that it returns more genes - please see my previous answer, here: A: Hub selection in WGCNA
There are different ways to calculate hub scores. WGCNA's implementation is one way. I allude to others in my tutorial: Network plot from expression data in R using igraph
Kevin
Thank you Kevin! I will see iT. By the way, what is your opinion about criteria of kME ≥0.85 and the top 10% of the gene list inside the module? Thank you!
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