Hello, I performed WGCNA on RNA-Seq data of 55 samples and used the code exactly as provided at the WGCNA website for the network analysis of the female mice data. There are three issues I am not sure about:
1) According to the tutorial recommendations I would need to choose a soft thresholding power of 3, since it reaches already R^2 of 0.8 and is also the maximum. However, the power recommendations in the table of the FAQs suggest a power of 6-12 for my sample size. What would you recommend?
2) I am using about 20,000 genes as input, and both the signed and the unsigned network analysis yield 4 or 5 modules containing thousands of genes (the largest module contains 9,000 genes), and about 15 modules containing hundreds of genes. Should I be concerned about the large modules?
3) I want to correlate the gene modules with continuous (BMI), categorial (e.g. smoking habits) and binary variables (e.g. mutation yes/no). What correlation is the best for all types of variables? bicor(x,y, robustY = FALSE, maxPOutliers = 0.05) or simple pearson? Or is a separated correlation according to variable type the best? I have NAs in every kind of variable.
Thank you in advance