Hi Andrew,

I compared two groups using NBS and T-test, but the random and actual sizes are hard to explain. For one direction (e.g., 1 -1), the random and actual sizes are both 0, and the p-value is 1. However, it still showed a subnetwork even though the P-value is 1 after the permutation. For another direction (e.g., -1 1), the random and actual sizes are both large, almost over 2000. The subnetwork that NBS reported consisted of all nodes (90) and 3438 edges. I also adjusted the threshold from small (e.g., 1) to large values (e.g., 15), but the results were the same for both directions.

I have already used NBS for a while, but I have never met this issue before. Hence, I am lost here, could you please give me some suggestions to solve this issue? Thank you so much!

Best,
Gucy