I am trying to run WGCNA analysis on a microarray dataset. I have been following this tutorial: https://bioinformaticsworkbook.org/tutorials/wgcna.html#gsc.tab=0 I am confused about the subheading "Relate Module (cluster) Assignments to Treatment Groups." The question is: Can we see how each module is associated with the treatment group as a measure of correlation? My question arises since the name of a 'treatment group' essentially is not a numeric value that can be used to calculate the correlation. From what I understand in the tutorial, the name 'corr' and values (-1,1) are the input given in the code, not the actual correlation function used. please let me know if I am understanding this correctly (or not).
Also requesting to share some resources if there are any on the same. Thanks in advance!
Hi andres, Thank you for your invaluable responses on Biostar regarding WGCNA. I've gained a lot of knowledge from the insights you've shared in your posts. I'm a bit confused about my WGCNA analysis. I've been proceeding with both DE mRNA and DE lncRNA in a single VST normalized matrix for co-expression studies, However, when it comes to module-trait analysis, should I consider only DE mRNA or both?
Hi,
First of all, you should never use DEGs for WGCNA. See Kevin Blighe answer: link.
You should consider both because the module eigengenes used in the module-trait analysis are calculated from co-expression modules including both lncRNA and mRNA.