Hi all, I'm trying to use WGCNA analysis on both proteomics and RNA-seq data. I succeed in getting some modules that are correlated to clinical traits, but most of the modules were not significant. Even these modules which were significant, when I have tried to enrich the modules to the trait, I haven't got a lot of processes. the bigger problem from me was in the RNA-seq. I have tried filtering of genes with some options and I wondering, which one is the best to get better results. scale-free topology got almost 0.9... from your experience, what should I use to filter genes (low variation/ filter 0 values?) should I change specific parameters in some functions to construct a better co-expression network? If you can share with me more tips, I'm will be glad to hear, I'm new in R and trying to improve my abilities and result Thanks a lot! Sagi
