I used the Network Analyzer core app to get the basic parameters of an undirected network on Cytoscape. All the parameters are satisfactorily measured like the degrees, centrality measures of each node, diameter of the network etc. However, the clustering co-efficient of each node is given as 0.0 and the overall clustering co-efficent of the network is calculated as 0.0. I am next going to compare my network with a random network and network co-efficient is a key measure that I would like to compare in order to prove that my network is a scale free network. What could be going wrong. There are 361 nodes and 695 edges in my network. Any ideas are appreciated
Already answered on cytoscape-helpdesk, but for completeness, I've repeated it here....
Hi Rahul,
So, with 361 nodes and 695 edges, the average degree of your network is 2. that could certainly lead to a cluster coefficient of 0.0 since that measure depends on the extent to which a node's neighbors are connected. Look for nodes that have well connected neighbors and take a look at the clustering coefficient of those nodes.
First, understand that comparing your network with a single random network will not yield a p value (or if it does, it's honestly worthless). You need to generate a distribution of random networks, then compare your network to the distribution to see if you are outside of the distribution. Take a looks at Tosadori, et al., 2016 for their discussion on the use of Network Randomizer with cytoscape.