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