I am trying to build gene co-expression networks with WGCNA by combining in-house and publicly available RNA-seq datasets. I am interested in identifying gene networks associated with different environmental conditions. I used SVA to adjust for batch effects and "protected" different environmental conditions in the model as I don't want to lose information about them. However, when I used the "batch-adjusted" data to create networks, all the scale-free topology indices were negative (max = -0.05).
I tried generating the networks with softpower = 16 as it is suggested for sample sizes 20-30. However, only five networks were generated which is far less than I expected.
What might be the reason for getting negative scale-free toplogy indices?
Can combining studies from different environmental conditions cause the networks to be not biologically meaningful?