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Hi, I'm having problem with picking soft threshold power in WGCNA. They all have SFT. R. sq lower than 0.8, so I have trouble with picking soft threshold power. What power should I pick?
Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
1 1 0.73200 2.3400 0.896 704.0 734.00 995.0
2 2 0.30700 0.5700 0.641 407.0 424.00 700.0
3 3 0.00023 0.0131 0.383 265.0 271.00 522.0
4 4 0.08980 -0.2580 0.504 185.0 186.00 408.0
5 5 0.22200 -0.4520 0.619 135.0 133.00 328.0
6 6 0.32800 -0.6270 0.685 103.0 99.50 269.0
7 7 0.41800 -0.7310 0.759 80.5 76.00 225.0
8 8 0.48800 -0.7980 0.823 64.4 59.70 191.0
9 9 0.53600 -0.8660 0.847 52.4 47.60 164.0
10 10 0.57100 -0.9300 0.869 43.4 38.90 142.0
11 12 0.62500 -0.9900 0.913 30.8 26.80 110.0
12 14 0.67400 -1.0300 0.940 22.8 18.90 87.1
13 16 0.71800 -1.0700 0.954 17.4 13.70 70.4
14 18 0.75200 -1.0900 0.956 13.7 10.10 57.9
15 20 0.77800 -1.1400 0.973 10.9 7.73 49.1
This is not a bioconductor pacakge, but have you considered that something might be off with your data? Do you have enough samples of each category? Where all normalized the same way?