Dear Andrew, 

Thank you for your kind response! 
I just ran the NBS without covariates, and it shows significant subnetworks for the contrast of Disease > Control. 
However, with the covariates, it shows opposite subnetworks of Control > Disease. 
In this case, is it okay to interpret confounds have a significant impact? 

One more thing, 
 As I ran the t-test for each edge from the significant subnetworks with controlling the covariates, still some edges show opposite directionality, which is Disease > Control. 
Is this also possible, even though I controlled all the covariates? 

Thank you! 
 
Sincerely, 
Jean