Question: problem for finding soft power for constructing network in WGCNA algorithm

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modarzi •

**10**wrote:Hi,

For constructing network I used WGCNA alghorithm.So,before constructing network, I have to determine SFT index. for that, I ran below code:

sft = pickSoftThreshold(MyData, powerVector = powers, verbose = 5) So I get 10 option as below: Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k. 1 1 0.439 -7.21 0.715 3280.000 3210.000 4890.0 2 2 0.931 -5.79 0.970 614.000 579.000 1460.0 3 3 0.974 -4.44 0.991 150.000 133.000 602.0 4 4 0.968 -3.61 0.984 44.600 36.600 304.0 5 5 0.957 -3.08 0.978 15.700 11.600 176.0 6 6 0.943 -2.72 0.972 6.420 4.140 112.0 7 7 0.922 -2.48 0.960 2.980 1.620 76.2 8 8 0.926 -2.25 0.964 1.550 0.688 54.4 9 9 0.922 -2.09 0.952 0.887 0.310 40.4 10 10 0.958 -1.88 0.957 0.552 0.147 30.9

so, after that for determining power value I have to plot based on below code:

par(mfrow=c(1,2)) # SFT index as a function of different powers plot(sft$fitIndices[,1],sign(sft$fitIndices[,3])*sft$fitIndices[,2], xlab="Soft Threshold (power)",ylab="SFT, signed R^2",type="n",main=paste("Scale independence")) text(sft$fitIndices[,1],sign(sft$fitIndices[,3])*sft$fitIndices[,2],labels=powers,col="red") # this line corresponds to using an R^2 cut-off of h abline(h=0.90,col="red")

My problem is in Scale independence plot. all power values are upper 'abline' and my abline has no intersect to any value. Now, based on this situation for constructing network, I have to consider maximum 'SFT.R.sq' as selected power or not? if this is true, should I select my power equal 3?

I appreciate if anybody share his/her comment with me.

Best Regards,

Mohammad

P.S: my network is unsigned.