I have two expression matrices (normalized, using dChip), with the same data except that in one of them , the expression values are log-transformed. I am trying to perform WGCNA analysis on them and getting different plots for scale independence.
First image: For the log-transformed values, some of the power-values (like 9,10) seems to approach 0.9 (red line corresponds to 0.9).
Second image: For the plot in which the data is not log-transformed, none of the power-values are falling beyond R^2>=0.9, (the red line corresponds to 0.8). I am in a dilemma as to which beta threshold I should consider and whether one should take log-transformed values or not for the analysis