Question: WGCNA: Output gene lists from consensus network modules
2
gravatar for RossCampbell
2.6 years ago by
RossCampbell140
USA/Frederick
RossCampbell140 wrote:

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?

wgcna • 2.9k views
ADD COMMENTlink modified 16 months ago by baldauf20 • written 2.6 years ago by RossCampbell140
1
gravatar for baldauf
16 months ago by
baldauf20
baldauf20 wrote:

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

ADD COMMENTlink modified 16 months ago • written 16 months ago by baldauf20

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

Kevin

ADD REPLYlink written 9 months ago by Kevin Blighe44k
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