Hi, I created a consensus modules from 2 coexpression networks from different transgenic animals, and I would like to see which of those modules are not preserved in wild-type by measuring module preservation between consensus and wt.

Is it possible to do this? I am asking because module preservation requires the expression data, which in case of the consensus network is 2 sets.

Thanks!

Yes, you have two reference data sets and one test data set. Run module preservation between each of the reference data sets and the test data set, so you get two sets of preservation statistics. You can look for modules for which the preservation is low in both preservation calculations. My intuition is that the preservation stats should be fairly similar, more so the density than the connectivity ones, so if a module is not preserved in calculation with one reference set it should also be non-preserved, or at most weakly preserved, in the calculation with the other reference set.