This is regarding the package WGCNA (Weighted gene coexpression network analysis) in R. I have been trying to use this package on my data.
I use the blockwiseModules() function to get my modules. WGCNA identified some modules. When I look into the membership values of the genes, they are high. On the other hand, when I do the pairwise correlation analysis of the genes within a particular module, they are extremely low. I get the modules using $colors so they are after merging as far as my understanding goes. I tried the same with the sample data provided with the package (female mice liver data) and I observe similar pattern, they are not as low as they are in my data but they are all not above 0.8 which is my cut off (merCutHeight=0.2). I am unable to understand this statistical point of the results. Has someone faced a similar situation when working with the package? Can someone throw some light on this.
Thanks in advance.