TABLE 1.

Identification of differentially expressed genes

	No assumption of equal variance			Assume equal variance				No. of probe setsa
	FDR = 0.05	FDR = 0.10	FDR = 0.25	FDR = 0.05	FDR = 0.10	FDR = 0.25	% probe setsa	B73 > Mo17	Mo17 > B73
B73 vs. Mo17
11-day seedling	1633	3284	7400	3135	4784	8726	9.3	767	866
Immature ear	740	1732	4749	2031	3209	6269	4.1	442	298
19 DAP embryo	3264	5355	8907	5108	6786	9935	18.4	1437	1827
B73 × Mo17 vs. Mo17 × B73
11-day seedling	0	0	0	0	0	0	0	0	0
Immature ear	0	0	0	0	0	0	0	0	0
19 DAP embryo	0	0	0	0	0	214	0	0	0

Analysis of differential expression in B73 relative to Mo17 or B73 × Mo17 relative to Mo17 × B73. Differentially expressed genes were identified using a one-way ANOVA to test GC-RMA values. Tests were performed with and without an assumption of equal variance with a Benjamini–Hochberg multiple testing correction and varying false discovery rates (FDRs).

^aThese calculations are based on the list of differentially expressed genes identified using no assumption of equal variance and an FDR = 0.05.