Table 4.

Effect of decreasing number of replicates on significantly differentially expressed genes while maintaining 100 and 25% of the reads.

Number of replicates (ATCC10792)*	Differentially expressed genes (FDR 5%, two-fold)		Genes commonly detected with all four reps
	100%Reads	25%Reads	100%Reads	25%Reads
4 (1A, 2A, 3A, 4A)/(9A, 10A, 11A, 12A)	887	696	100% (887)	100% (696)
3 (1A, 3A, 4A)/(9A, 11A, 12A)	885	689	83.5% (741)	84.9% (591)
2 (1A, 4A)/(9A,12A)	720	501	68.4% (607)	59.3% (413)

^*All combinations of available replicates were tested. Results for replicates with most similar read numbers are shown.