Generating descriptors at pathway level for further use to classification methods.

Question

[arronar]

Hello.

I'm having 6 different microrray experiments for 6 different drugs that treat the same disease. What I want to do now is to create some descriptors for each of these datasets at the pathway level.

As far as I read the literature, I decided to use the pathifier algorithm described in this article that produces for each pathway a PDS (pathway deregulation score).

Next I want to use these PDSs to build a classifier either using kNN / random forest etc.

Before start implementing it I wanted to ask here if anyone have any other idea or method to calculate descriptors (other than the pathifier's PDS).