enter code here

Hi,

Hope some knows how to help me.

I am running a WGCNA with 36 samples in RNA-Seq data and I am facing some difficulties to find the exact power in my analysis. My code is:

powers <- c(c(1:10), seq(from = 12, to=20, by=2))

sft <- pickSoftThreshold(datExpr1, powerVector = powers, verbose = 5, networkType = "signed")

I obtained this results:

Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.

 1  0.82700 11.0000          0.859  9450.0    9550.0  11200

 2  0.71700  4.6500          0.866  5810.0    5900.0   7990

 3  0.54500  2.3600          0.953  3780.0    3820.0   5990

 4  0.24500  1.1000          0.877  2580.0    2580.0   4640

 5  0.00385  0.0874          0.756  1830.0    1800.0   3690

 6  0.09260 -0.3660          0.719  1340.0    1300.0   3010

 7  0.27800 -0.6570          0.730  1010.0     948.0   2500

 8  0.41800 -0.8350          0.755   779.0     706.0   2110

 9  0.50700 -0.9430          0.782   613.0     533.0   1810

10 0.54800 -1.0500 0.791 490.0 410.0 1570

12 0.59700 -1.2200 0.811 328.0 250.0 1230

14 0.61900 -1.3300 0.823 230.0 159.0 989

16 0.65400 -1.3900 0.847 167.0 105.0 810

18 0.70500 -1.3900 0.881 125.0 71.3 674

20 0.74500 -1.3900 0.905 95.7 49.3 568

I tested a power from 20, but I obtained a strong correlation in grey module, so I decreased for power 16 to figure out and the same trouble repeated in my analysis. Now I have doubts if I will try running WGCNA with a power of 18 or if I increase the power to 40 to see if my mean k. improves.

Hope someone can help me.

Best,

Fernanda