WGCNA: Output gene lists from consensus network modules

Question

[RossCampbell]

I am using WGCNA to create a consensus network from two different gene expression data sets. I want to do some downstream analysis with the modules that came out of this, so I would like to output the genes comprising each module. I know how to do this when dealing with modules from individual networks as described in the tutorial, since there is just one gene list, simply matching the index between the gene and modules lists works fine. However, that's not feasible in the consensus since there are two different gene sets as input. So instead, is there a method somewhere in WGCNA that I haven't come across yet that will take each module from a consensus network and output the genes that comprise it?

Answer 1

[baldauf]

I found a solution in the this Tutorial "II.4. Relating consensus module to external microarray sample traits and exporting the results of network analysis" by Langfelder and Horvath. https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/index.html

[Kevin Blighe]

Tutorial now moved to: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/

Kevin