Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
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jol.espinoz ▴ 40
@jolespinoz-11290
Last seen 6 months ago

Why isn't it just the R^2 value and instead multiplying -sign(slope) * R^2 ?

What does a negative scalefree topology in this event mean?

I'm following the tutorial here: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-02-networkConstr-man.pdf

# Scale-free topology fit index as a function of the soft-thresholding power
plot(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2], #<--------- this line right here

xlab="Soft Threshold (power)",ylab="Scale Free Topology Model Fit,signed R^2",type="n",
main = paste("Scale independence"));
text(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2],
labels=powers,cex=cex1,col="red");

enter image description here

Network StatisticalMethod WGCNA ExpressionData • 184 views
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