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jol.espinoz
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40

@jolespinoz-11290
Last seen 3.3 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");
```