WGCNA network from Adjacency or TOM matrix · Biostar

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WGCNA network from Adjacency or TOM matrix

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

wgcna network

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updated 2.3 years ago by andres.firrincieli

• written 2.3 years ago by Milly •

1 answer

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

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written 2.3 years ago by andres.firrincieli

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