We describe methods used and some results in a study of schizophrenia in a population of affected and unaffected participants, called patients and controls. The subjects are characterized by diagnosis, genotype, brain anatomy (MRI), laboratory tests on blood samples, and basic demographic data. The long term goal is to identify the causal chains of processes leading to disease. We describe a number of preliminary findings, which confirm earlier results on deviations of brain tissue volumes in schizophrenia patients, and also indicate new effects that are presently under further investigation. More importantly, we discuss a number of issues in selection of methods from the very large set of tools in data mining and statistics.