Hi,

I have a RNA-seq dataset from human immune cells extracted from lung cancer and normal tissue, total 22 paired samples (11+11). 11000 genes are differentially expressed. A WGCNA analysis results in one module of particular interest (Turquoise module, 2000 genes), which is not significantly correlated to the traits of interest (T-high, til-high, B-high), but highly correlated to the cancer/control condition (disease-state-bin).

I want to investigate correlation to the traits of interest for genes or clusters of genes within the turquoise module, ideally to identify a subgroup of genes within the turquoise module that is correlated to the particular traits, for GO-term and enrichment analysis. Is this advisable, and how do I do this (in R)?

Kind regards, Anders