Table 5 Computation time in minutes to estimate permutation P-values for the condition × gene interactions for each plate (a total of ∼1 million interactions)

Plate	1	2	3	4	5	6	Total
MLM	2.82	2.78	3.46	3.28	2.82	3.00	18.16
S scores	77.62	72.59	93.37	94.22	76.31	77.32	491.42

The computational advantages of matrix linear models are even more apparent when permutation P-values are desired. MLM, matrix linear model.