Table 4.

Comparison between the GPA and housekeeping gene normalizations based on simulated boutique array data with the Balagurunathan's method. The data sets are simulated without or with dye bias and include 1000 genes in 10 slides with 60% differentially expressed genes. The ratios of up-regulated to down-regulated genes are 5:5, 7:3, and 9:1, respectively.

Ratio(1)	Method	Without dye bias		With dye bias
		ν(2)	β(2)	ν	β
5:5	Raw	0.1147	0.008632	0.1144	0.007297
	Housekeeping gene	0.1133	0.008569	0.1164	0.007326
	GPA	0.03285	0.002833	0.03349	0.002584
7:3	Raw	0.1139	0.007859	0.1186	0.007902
	Housekeeping gene	0.1157	0.007937	0.1195	0.007427
	GPA	0.0288	0.00315	0.03133	0.003334
9:1	Raw	0.1172	0.007659	0.1178	0.007916
	Housekeeping gene	0.1187	0.006898	0.1152	0.009463
	GPA	0.02785	0.004814	0.02802	0.005119

(1) Ratio of up- to down-regulated genes

(2) ν and β : the median of variance and bias, respectively, of MSE