WGCNA network from Adjacency or TOM matrix

Question

[Milly]

Hello, I want to reproduce and study the gene co-expression networks obtained from WGCNA and I dont know if I shoud use the adjacency matrix or the TOM matrix to extract the networka and analyse them. To contextualise, I have 18 samples (6 samples x 3 traits). As far as I know, I can use NetworkX package in Python to examine different things like hub genes, centrality (maybe you can advise me other measures because I am just starting at networks analysis). My question is whether I should use adjacency or TOM matrix.

Thank you in advance

Answer 1

[andres.firrincieli]

Since the module detection is performed on the TOM, you should go for the TOM.