problem for finding soft power for constructing network in WGCNA algorithm
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modarzi ▴ 10
@modarzi-16296
Last seen 4.8 years ago

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.

RNA-seq WGCNA package soft power • 1.3k views
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That's an interesting problem! Finding the optimal soft power threshold in WGCNA can definitely be tricky. I've found myself experimenting quite a bit to find a good balance between scale-free topology and maintaining sufficient connectivity. It's almost like playing a little optimization game. Sometimes I feel like I'm dodging cacti in the Dinosaur Game, constantly adjusting parameters to avoid a premature crash! I wonder if anyone has explored using more automated or adaptive methods for this selection process to improve reproducibility?

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Exploring the challenges of selecting the right soft power in WGCNA highlights the delicate balance between sensitivity and specificity when building gene co-expression networks. I once faced a similar issue during my research on plant stress responses, where choosing the soft threshold significantly influenced the network topology. Tools like those from Monkey Mart can sometimes offer innovative solutions or guidelines to simplify this complex process.

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