Table 1. Summary of simulations used in the study.

Inspection intent	Number of samples in condition 1	Number of samples in condition 2	Number of genes	Fraction of DE genes	Fold-change between two conditions	Simulation type
cdev as a function of normalization quality	20	20	{2000, 10000, 20000, 50000}	0.5	4	Homogeneous fold-change
	20	20	20000	0.5	{1.5, 2, 3, 4, 5, 6, 7, 8}	Homogeneous fold-change
	20	20	10000	{0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9}	4	Homogeneous fold-change
	20	20	{2000, 10000, 20000, 50000}	0.5	Continuous	Heterogeneous fold-change
	20	20	10000	{0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9}	Continuous	Heterogeneous fold-change
Concordance of cdev and fold-change MSE	15	15	4000	{0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9}	Continuous	Heterogeneous fold-change
Use of cdev to compare normalization methods	20	20	10000	{0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9}	Continuous	Heterogeneous fold-change