I used different algorithms for splitting my large gene network into different sub-networks using Cytoscape. I compared the modularity scores and decided that the algorithm with the best modularity score will be used for clustering the network.

My colleague came up with the argument that modularity scores can only be compared for different number of clusters being created by the same algorithm.

So, my question is if modularity scores can be used to compare between different algorithms or only in the case of the same algorithm producing different number of clusters.