Hi all, I wondered if a positive correlation for a module in the Heatmap indicates that genes within this module are up-regulated for the particular trait for which the correlation values is positive? Or does it not tell anything about up-or-down-regulation compared to other traits? I don't have continuous variables, but groups.
I do find that genes which are up-regulated in limma for a given contract belong to the modules which show negative correlation in WGCNA for the same group, how can this be? Should be opposite?