HI ,

I am a noob statistician and I am trying to build a gene co-expression network using pearson's correlation as a distance metric in my data. As I was doing this I caculated the correlation matrix which has values from [-1,1] and then squared this to make it [0,1] and then applied a threshold of 0.7 (totally arbitrary) and built a network.

When I was researching, I came across the package "coexnet" which does this in one-step. However when i compared the results they are varying. When I tried to look into the source code - I found this line.

```
simil <- abs(cor(t(difexp),use = "pairwise.complete.obs")) # line nbr 82 in the internalFunctions.R file
```

The author seems to have taken an absolute value.

What is the advice in this instance? Do we take the abs or square it? To me the negative values of r matrix means they are dissimilar which is now low when we do an abs.

Thanks in advance!