Question: problem for finding soft power for constructing network in WGCNA algorithm
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gravatar for modarzi
15 months ago by
modarzi10
modarzi10 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.

ADD COMMENTlink written 15 months ago by modarzi10
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