Why Wgcna Does Not Assign A Gene To The Module Of Highest Module Membership

Question

[heartheone]

I am using wgcna in co-expression analysis. I noted that one of the probe,

ILMN_1781516

 MM.pink:  0.826870232    .                           p.MM.pink:1.28E-15                                                          
  MM.black: 0.807209729                                p.MM.black:1.97E-14

I thought this probe should be assigned to module pink, but actually it belongs to module black as the geneinfo file generated by WGCNA. I wonder what goes wrong? Thanks!

hartblue

[aesteve]

Did you resolved your question?

I have exactly the same problem.

i.e, gene Traf6 in my dataset:

kME.cor red = 0.5369
kME.cor lightgreen = 0.6913
kME.cor grey60 =0.5419

and the software assigns Traf6 to the red module. Why?

Answer 1

[magdalena.nta]

Hi,I'm a bit late to this thread, but in case someone else comes across this, Peter Langfelder answered this question on this post.

To summarize his answer, he says this discrepancy between assigned modules and modules with the highest module membership can happen because WGCNA assigns modules using the Dynamic Tree Cut algorithm based on the Topological Overlap Matrix, which is similar but not equal to the correlation metric. He ends up by saying "In all, I don't worry about the module assignment vs. max. kME differences in my own analyses, and I recommend not worrying it about it to others as well."

So I guess that's what I'll do.