Question: How does WGCNA decide which genes are connected?
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gravatar for jolespin
4.1 years ago by
jolespin130
United States
jolespin130 wrote:

I'm using the Weighted Gene Coexpression Network Analysis package (WGCNA) in R and I am trying to figure out how the adjacency matrix is defined.

I understand how the correlation matrix is created along with why the power is used but adjacency matrices should be either 1 or 0.

Why are there still continuous values? How does it choose a cutoff later?

I can understand that it's maybe a weighted adjacency matrix but there isn't an option to make it binary and that is needed for the topological overlap matrix calculation (TOM)

ADD COMMENTlink modified 3.2 years ago by sina.nassiri60 • written 4.1 years ago by jolespin130
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gravatar for sina.nassiri
3.2 years ago by
sina.nassiri60
Switzerland/Lausanne
sina.nassiri60 wrote:

An adjacency matrix is a square, symmetric matrix with entries between 0 and 1 (don't have to be 1s and 0s), and the TOMsimilarity() and TOMdist() functions in WGCNA both handle non-binary adjacency matrices.

ADD COMMENTlink written 3.2 years ago by sina.nassiri60
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