This article has good general advice about how to run a statistical analysis, such as Rule 1: Statistical Methods Should Enable Data to Answer Scientific Questions.
Robert E. Kass, Brian S. Caffo, Marie Davidian, Xiao-Li Meng, Bin Yu, Nancy Reid. Ten Simple Rules for Effective Statistical Practice. PLOS Computational Biology. 2016 (June 9). Available at http://dx.doi.org/10.1371/journal.pcbi.1004961.