Repetition Mixed Model Wilcoxon Signed-Rank Test
1 0.041 0.139
2 0.043 0.138
3 0.049 0.137
4 0.044 0.136
5 0.045 0.135
6 0.040 0.135
7 0.041 0.134
8 0.044 0.143
9 0.043 0.134
10 0.054 0.138
Overall 0.044 0.137
For each repetition, the simulation dataset consisted of 744 gene sets and P-values for patient specific pathway activities were calculated for each of the 18 patient samples. Therefore the type I error rates were calculated based on a total of 13392 tests (744 gene sets ×18 patient samples) for each repetition.
Table 1: Type I error rate for Mixed Model 1 and the Wilcoxon Signed-Rank test ( α = 0.05).