I am interested in comparing the effects of preprocessing. I am exploring two analysis method variants that produce different statistical results. Visually, the residual mean square is much higher for one method than the other. I would appreciate advice as to how to quantitatively compare the residuals, especially how to properly correct for the multiple comparisons/resels. Please let me know if there is better way of assessing possible reductions variability of one method relative to another.

Thank you!

Bennett Landman