Network Analyzer in Cytoscape

Question

[The Last Word]

Hi,

Anyone who has used Cytoscape might be familiar with the Network Analyzer tool in Cytoscape which is used to calculate the degree distribution of the network. I did the same, plot the degree distribution and fit a power law y = ax(squared b) where b is the slope. Cytoscape gives the R-squared and correlation values of the network. By my understanding, The correlation coefficient (R) is squared to obtain the coefficient of determination (R-squared). However, none of my networks have the R-squared value as a square of the correlation value. For example, this is the correlation and R-squared values of three of my networks.

R-squared Correlation

0.684 0.963

0.532 0.942

0.621 0.949

Am I getting this wrong and does correlation mean something different and not correlation coefficient (R) in Cytoscape?

Answer 1

[Jean-Karim Heriche]

If you're fitting a power law, the coefficient of determination is most likely calculated on log(data). This is probably mentioned somewhere in the docs.
EDIT: Found it mentioned in the docs here.

[The Last Word]

Hi Jean, just to clarify, the correlation refers to the correlation coefficient right? It just says correlation and I am confused as to if that stands for something else.

[Jean-Karim Heriche]

Yes this is the correlation coefficient.