Modules differential co-expression explanation

[adomingues]

Hi @Kumquatum,

I trying the GWENA package which seems very intuitive and easy to use - thank you! My goal s detect gene models between two conditions, specially identify genes which reflect a mutant state (vs control).

The one aspect I am struggling with is the modules differential co-expression. In my experiment I have two conditions, mut and wt, for which 6 and 2 modules were identified with:

lapply(
   se_expr_by_cond, build_net,
   cor_func = "spearman", 
   n_threads = threads_to_use,
   keep_matrices = "both"
)

But when I ran the differential analysis using wt as a reference, the plot_comparison_stats shows the 2 wt modules. Is this expected? Since I am interested in those gene modules which are "specific" to the mutant, I naively thought that I would get those 6(+2) which reflect this.