I'm just getting into using WGCNA and had a question about my last run through. I'm looking at differences between two species in brain gene expression using RNAseq data. WGCNA produced 4 modules including the set of unassigned genes (labeled module 0 or the grey module).
The grey module was highly and significantly correlated with species identity, whereas none of the other modules had any apparent relationship.
It makes intuitive sense to me that any genes related to species differences would have a lot of noise and, thus, be difficult to assign to a module when grouping together both species.
My question is if this interpretation is correct and, if so, if it makes more sense to use a consensus module approach to compare species?
Thanks very much for any help!