Table 7.

Comparison of the differential expression analysis between HG-U133Plus2 and Hugene 1.0 ST arrays preprocessed with several popular algorithms

Method	Data	Diff. expr.	m1 m9	m2 m8	m3 m7	m4 m6	m1 m6	m4 m9	m1 m4	m6 m9	m1 m5a	m5a m9	m1 m5b	m5b m9	m1 m5c	m5c m9
MAS 5 1-Step Tukey-Biweight	PM	Student	0.51	0.49	0.46	0.36	0.48	0.52	0.49	0.40	0.52	0.55	0.54	0.56	0.49	0.45
		Win. t	0.60	0.57	0.54	0.46	0.56	0.62	0.59	0.48	0.61	0.63	0.63	0.64	0.58	0.58
		Reg. t	0.54	0.52	0.49	0.46	0.52	0.58	0.56	0.42	0.57	0.60	0.59	0.60	0.55	0.54
	PM	Student	0.48	0.49	0.49	0.42	0.50	0.50	0.44	0.40	0.44	0.46	0.48	0.47	0.45	0.49
	Norm	Win. t	0.57	0.57	0.59	0.53	0.59	0.61	0.55	0.51	0.55	0.57	0.58	0.58	0.55	0.60
		Reg. t	0.50	0.51	0.56	0.53	0.54	0.58	0.52	0.47	0.52	0.55	0.55	0.56	0.49	0.59
Plier	Raw	Student	0.51	0.59	0.48	0.41	0.52	0.49	0.40	0.43	0.57	0.59	0.56	0.56	0.46	0.49
		Win. t	0.58	0.64	0.54	0.49	0.59	0.58	0.52	0.51	0.62	0.64	0.62	0.62	0.56	0.60
		Reg. t	0.56	0.64	0.54	0.52	0.58	0.58	0.52	0.51	0.61	0.65	0.60	0.62	0.55	0.60
dChip Li-Wong MBEI	PM	Student	0.46	0.49	0.41	0.43	0.48	0.47	0.41	0.36	0.31	0.44	0.41	0.49	0.40	0.49
	Norm	Win. t	0.54	0.55	0.49	0.51	0.55	0.56	0.50	0.47	0.39	0.52	0.50	0.58	0.47	0.58
		Reg. t	0.48	0.51	0.45	0.51	0.53	0.52	0.46	0.41	0.30	0.49	0.45	0.55	0.41	0.55
RMA Median-polish	Norm	Student	0.54	0.55	0.55	0.46	0.52	0.54	0.44	0.46	0.45	0.52	0.48	0.52	0.49	0.52
		Win. t	0.64	0.64	0.64	0.56	0.62	0.65	0.56	0.58	0.57	0.64	0.59	0.63	0.59	0.64
		Reg. t	0.65	0.66	0.66	0.60	0.64	0.66	0.58	0.60	0.59	0.67	0.62	0.65	0.61	0.67
GCRMA Median-polish	Raw	Student	0.58	0.61	0.57	0.46	0.52	0.60	0.43	0.60	0.49	0.63	0.54	0.65	0.48	0.57
		Win. t	0.63	0.64	0.59	0.49	0.56	0.64	0.49	0.64	0.54	0.67	0.61	0.68	0.54	0.63
		Reg. t	0.63	0.65	0.60	0.52	0.56	0.65	0.52	0.65	0.52	0.68	0.62	0.69	0.52	0.64
	Norm	Student	0.50	0.49	0.48	0.46	0.49	0.51	0.47	0.51	0.47	0.50	0.48	0.51	0.47	0.49
		Win. t	0.60	0.59	0.59	0.55	0.57	0.61	0.54	0.60	0.56	0.61	0.58	0.60	0.56	0.61
		Reg. t	0.59	0.61	0.61	0.59	0.59	0.62	0.56	0.63	0.58	0.64	0.60	0.63	0.57	0.62

We compared the results of the differential expression analysis of the Tissue Mixture Study between HG-U133plus2 and Hugene 1.0 ST arrays, using Student t-test, Regularized t-test and Window t-test. Preprocessing was performed with several popular methods. For each combination of preprocessing/analysis steps (rows), and each comparison of mixtures (columns), Pearson's correlation coefficient has been computed on log10(p-values) between both types of arrays. Underlined characters highlight the top 5 correlation coefficients for each column. The best match table provided by Affymetrix has been used to map probesets between the two platforms. Raw/Norm labels refer to raw and normalized data, PM stands for PM-only methods.