I am analyzing RNA-Seq experiments using WGCNA. I am performing a consensus analysis of two different datasets.
When choosing soft-thresholding power using networkType="signed hybrid", one dataset (about 40 samples) exceeds SFTI of 0.9 at 12, however, another dataset (about 25 samples) exceeds at 26.
I am thinking about going to pick 26 as this power can ensure the scale-free topology for both networks, however, the official Q&A stated that the reasonable power is "less than 15 for unsigned or signed hybrid networks, and less than 30 for signed networks", in which 26 is high for signed hybrid network I'm intending to construct. I think the high power needed for the latter dataset is caused by an interesting biological variable that I do not want to remove effect.
In this case, is it reasonable to choose high power like 26? Are there any disadvantages or points that should be taken care of, when choosing high power?