Running HotNet2 over a custom network

[aallahyar]

I would like to report an issue (or maybe my lack of understanding) on

hotnet2/hotnet2/heat.py

Line 23 in 29fe555

min_score = min([score for score in heat.values() if score > 0])

This line is where my execution of HotNet2 halts. Further check revealed that none of values in "heat.values()" is larger than 0. In turn, it produces an empty list and "min" function raise s an exception.

If all values are zero (which is the case for me), it means that none of genes on that specific subnetwork have heat. So I wonder how this subnetwork became a significant hit. Thats where my confusion starts.

Would you please help figure out what I am missing?

Thanks!

[krassowski]

See very similar discussion on: https://groups.google.com/forum/#!topic/hotnet-users/wV9NF-u9Qtw.
It may help you or may not, but it is related to the same line and the same exception.

[aallahyar]

Thanks @krassowski I think you are pointing to the right direction.
However, I am using an identical (weighted) network with different thresholds to make the network binary. So the node and score identifiers has not changed.

At the same time, I realised that once the threshold is too conservative, then the chance of raising this error increases. So I am expecting that somewhere inside HotNet2, there is a step that fails when few number of genes are connected or have small score.