I am trying to run WGCNA on variance stailized ran-seq data ( DESeq2 ) on 66 samples ( 33 treated vs 33 untreated ). When I try to chose a soft threshold, I see that the SFT.R.sq does not reach 0.9, which I see in most of the tutorials. According to my understanding, the softPower is chosen when the SFT.R.sq reaches 0.9.

This is my output.

pickSoftThreshold: will use block size 1961.
 pickSoftThreshold: calculating connectivity for given powers...
   ..working on genes 1 through 1961 of 22812
   ..working on genes 1962 through 3922 of 22812
   ..working on genes 3923 through 5883 of 22812
   ..working on genes 5884 through 7844 of 22812
   ..working on genes 7845 through 9805 of 22812
   ..working on genes 9806 through 11766 of 22812
   ..working on genes 11767 through 13727 of 22812
   ..working on genes 13728 through 15688 of 22812
   ..working on genes 15689 through 17649 of 22812
   ..working on genes 17650 through 19610 of 22812
   ..working on genes 19611 through 21571 of 22812
   ..working on genes 21572 through 22812 of 22812

   Power SFT.R.sq   slope truncated.R.sq mean.k. median.k. max.k.
1      1 0.000491 -0.0301          0.833 4700.00  4.65e+03 8210.0
2      2 0.603000 -0.9330          0.878 1610.00  1.43e+03 4330.0
3      3 0.762000 -1.1500          0.916  719.00  5.37e+02 2680.0
4      4 0.801000 -1.2700          0.927  375.00  2.28e+02 1820.0
5      5 0.830000 -1.3300          0.943  216.00  1.05e+02 1300.0
6      6 0.822000 -1.4100          0.939  134.00  5.24e+01  975.0
7      7 0.820000 -1.4600          0.944   87.60  2.75e+01  751.0
8      8 0.820000 -1.5000          0.949   59.60  1.50e+01  591.0
9      9 0.830000 -1.5200          0.959   41.80  8.53e+00  472.0
10    10 0.843000 -1.5300          0.970   30.10  4.99e+00  383.0
11    12 0.842000 -1.5800          0.974   16.60  1.82e+00  260.0
12    14 0.848000 -1.6000          0.981    9.79  7.24e-01  182.0
13    16 0.838000 -1.6500          0.975    6.05  3.05e-01  131.0
14    18 0.837000 -1.6600          0.980    3.89  1.34e-01   96.8
15    20 0.839000 -1.6700          0.982    2.58  6.17e-02   72.5

Does this mean my data has more noise ?

Please read WGCNA FAQ, point 6.

Peter