i am trying to run WGCNA on my rnaseq dataset (20 samples, 2 conditions 10 obs each). I had a batch effect corrected with edgeR.
When I try to apply the soft threshold on my dataset I run into the following dilemma: if I set the network type "unsigned" I obtain a soft threshold of 15. If I rather make it "signed" then even after a power of 30 it doesn't get a scale free topology index of 0.9.
My knowledge in statistics is limited, and I cannot understand the reasons for such a weird behavior.
Can anyone help?