Best way to organize data gathered during research?

What is the best and most scientific way to organize all the qualtative data gathered during research? I think this is important because with easy to understand research and data, it will be difficult to create accurate personas and user scenarios. I started using affinity diagraming to organize data gathered during user research, but I was wondering if anyone else had any other ideas. I feel that another scientific approach would really he helpful.

For example, I may have pages and pages of word and excel docs filled with research data. What is the best way to organize this so it actually makes meaningful sense?