Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
0
0
Entering edit mode
jol.espinoz ▴ 40
@jolespinoz-11290
Last seen 3.0 years 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 • 1.2k views
ADD COMMENT

Login before adding your answer.

Traffic: 784 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6