While clustering a network using Community Cluster (GLay) in ClusterMaker it gives a cluster number for each cluster. What does this represent? I Initially thought it to simple numbers to distinguish between two clusters but I saw that the cluster with highest node is at #2 while the other major cluster with slightly less nodes is #1. This makes me raise the question.
Parallel post in Cytoscape Google Forums
That's my concern. Even in their example problem in their paper I saw a similar situation.