Table 5.

Comparison between the GPA and housekeeping gene normalizations based on simulated boutique array data with the SIMAGE method. The data sets include 1000 genes in 50 slides with 60% differentially expressed genes and the ratios of up-regulated to down-regulated genes are 5:5, 7:3, and 9:1, respectively.

Method	5:5(1)		7:3(1)		9:1(1)
	ν(2)	β(2)	ν	β	ν	β
Raw	1.467	0.4234	1.178	0.4687	1.532	0.8552
Housekeeping gene	0.2055	0.4642	0.1842	0.478	0.176	0.9346
GPA	0.111	0.3402	0.1059	0.3296	0.1194	0.5331

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

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