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module and trait correlation for WGCNA

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!

treatment wgcna relation microarray module-treatment
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updated by andres.firrincieli andres.firrincieli • written by Shriyansh • Shriyansh

1 answer

Hi Shriyansh

The way the module-trait relationship works with categorical variables is well explained in this blog.

The following link (3.a) explains how to calculate the module trait relationship.

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written by andres.firrincieli andres.firrincieli

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?

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written by AS-git • AS-git

Hi,

First of all, you should never use DEGs for WGCNA. See Kevin Blighe answer: link.

However, when it comes to module-trait analysis, should I consider only DE mRNA or both?

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.

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written by andres.firrincieli andres.firrincieli

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