Table 3.

Comparing results of a separate analysis for each replicate

Replicate 1	Three-way crossclassification					Three two-way crossclassifications
	Replicate 3
	U		E
	Replicate 2		Replicate 2			Replicate 2				Replicate 3				Replicate 3
	U	E	U	E	Total	Replicate 1	U	E	Total	Replicate 1	U	E	Total	Replicate 2	U	E	Total
U	207	2	23	1	233	U	230	3	233	U	209	24	233	U	226	26	252
E	19	2	3	31	55	E	22	33	55	E	21	34	55	E	4	32	36
Total	226	4	26	32	288	Total	252	36	288	Total	230	58	288	Total	230	58	288

Crossclassification of the log-ratio for three replicates analyzed separately. A gene is classified as expressed if its posterior probability Pr{ℰ_g|Y_gj = y} exceeds 0.5 and as unexpressed otherwise. 

U, unexpressed; E, expressed.