Gene set analysis for longitudinal gene expression data

Table 3 Estimated type I errors for the permutation test of no treatment effect compared to GEE

distribution	n1	n2	G	permutation NP	GEE
Normal	5	6	20	0.041	0.097
	25	25	20	0.055	0.058
	45	50	20	0.047	0.056
	5	6	50	0.045	0.105
	25	25	50	0.058	0.053
	45	50	50	0.046	0.044
	5	6	100	0.033	0.087
	25	25	100	0.053	0.058
	45	50	100	0.047	0.045
Poisson	5	6	20	0.040	0.096
	25	25	20	0.058	0.055
	45	50	20	0.058	0.049
	5	6	50	0.041	0.109
	25	25	50	0.058	0.061
	45	50	50	0.052	0.062
	5	6	100	0.028	0.075
	25	25	100	0.053	0.063
	45	50	100	0.050	0.048
Exponential	5	6	20	0.040	0.101
	25	25	20	0.046	0.070
	45	50	20	0.047	0.062
	5	6	50	0.041	0.083
	25	25	50	0.048	0.056
	45	50	50	0.052	0.051
	5	6	100	0.041	0.087
	25	25	100	0.046	0.053
	45	50	100	0.044	0.059

The data from different genes and repeated measurements from the same gene have AR(1) correlation with correlation coefficient 0.5. The n1 and n2 are the sample sizes for treatment groups 1 and 2, respectively. G is the number of genes in the gene set. The estimate is at 0.05 level.