Hi all!
I've recently been working towards preparing a WGCNA as part of a publication, and can't seem to find a decent resource on the settings I should use while creating my blockwise modules. While looking over the literature, it seems like most people begin with the settings that the WGCNA tutorial suggests, and after running through that tutorial I end up with 32 modules. The problem lies with the overrepresentation of two modules in particular, brown and blue. This leads to a dendrogram looking like this:
I've seen a couple of different papers using other settings during module creation, but the justification to tweak the tutorial's recommendation seem weak at best, and like throwing crap at wall at worst. Outside of playing with settings until I find something I find arbitrarily pleasing is there a resource any of you know of that I can use to justify tweaking those settings?
Thank you so much for your help, you guys have been an absolute lifesaver since I started this project!
How many genes are are you using ? Is it RNA-seq ? How many samples do you have ? How did you normalize your data ?