Table 3.

Comparison of the differential expression analysis on Hugene 1.0 ST arrays preprocessed with affyILM and popular summarization procedures

Summary	Data	Diff. expr.	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
Average difference	Raw	Student	0.69	0.64	0.56	0.82	0.79	0.66	0.44	0.63	0.60	0.73	0.66	0.75	0.67
		Win. t	0.80	0.78	0.67	0.88	0.85	0.70	0.53	0.75	0.66	0.81	0.74	0.81	0.72
		Reg. t	0.66	0.66	0.54	0.82	0.79	0.63	0.48	0.73	0.59	0.77	0.67	0.75	0.58
	Scaled	Student	0.68	0.68	0.55	0.80	0.76	0.62	0.47	0.67	0.64	0.74	0.69	0.74	0.68
		Win. t	0.81	0.80	0.63	0.87	0.83	0.68	0.50	0.76	0.71	0.80	0.75	0.81	0.73
		Reg. t	0.70	0.70	0.51	0.80	0.76	0.59	0.41	0.66	0.59	0.71	0.64	0.73	0.65
Li-Wong MBEI	Raw	Student	0.74	0.68	0.62	0.84	0.79	0.69	0.45	0.63	0.64	0.75	0.70	0.76	0.72
		Win. t	0.82	0.79	0.71	0.86	0.83	0.70	0.53	0.71	0.68	0.80	0.77	0.79	0.74
		Reg. t	0.79	0.77	0.66	0.86	0.82	0.66	0.52	0.70	0.67	0.80	0.76	0.77	0.69
	Scaled	Student	0.71	0.70	0.58	0.77	0.74	0.61	0.46	0.63	0.63	0.72	0.68	0.71	0.68
		Win. t	0.81	0.81	0.65	0.83	0.80	0.66	0.50	0.72	0.70	0.78	0.75	0.77	0.72
		Reg. t	0.77	0.77	0.60	0.81	0.77	0.63	0.47	0.70	0.67	0.76	0.72	0.75	0.68
1-Step Tukey-Biweight	Raw	Student	0.77	0.71	0.66	0.87	0.83	0.72	0.48	0.67	0.66	0.78	0.73	0.80	0.73
		Win. t	0.84	0.82	0.73	0.91	0.88	0.74	0.57	0.76	0.70	0.83	0.79	0.83	0.76
		Reg. t	0.80	0.80	0.69	0.89	0.85	0.68	0.55	0.75	0.68	0.83	0.77	0.80	0.69
	Scaled	Student	0.76	0.75	0.62	0.84	0.80	0.67	0.53	0.70	0.69	0.78	0.73	0.78	0.73
		Win. t	0.84	0.84	0.68	0.88	0.85	0.72	0.55	0.78	0.74	0.83	0.78	0.83	0.77
		Reg. t	0.83	0.82	0.65	0.87	0.82	0.67	0.50	0.75	0.71	0.81	0.75	0.80	0.72
Median	Raw	Student	0.69	0.64	0.57	0.82	0.79	0.66	0.45	0.63	0.61	0.72	0.66	0.75	0.67
		Win. t	0.80	0.78	0.68	0.88	0.85	0.70	0.53	0.74	0.67	0.80	0.74	0.81	0.72
		Reg. t	0.77	0.76	0.63	0.86	0.82	0.65	0.50	0.73	0.64	0.79	0.72	0.78	0.66
	Scaled	Student	0.68	0.69	0.55	0.80	0.77	0.63	0.48	0.67	0.64	0.74	0.69	0.74	0.69
		Win. t	0.81	0.80	0.64	0.87	0.83	0.69	0.51	0.76	0.71	0.81	0.75	0.81	0.74
		Reg. t	0.78	0.77	0.59	0.85	0.80	0.63	0.45	0.72	0.67	0.77	0.72	0.77	0.69
Median-polish	Raw	Student	0.85	0.75	0.74	0.91	0.85	0.78	0.50	0.74	0.69	0.84	0.76	0.85	0.78
		Win. t	0.90	0.87	0.81	0.93	0.90	0.81	0.61	0.79	0.74	0.86	0.82	0.88	0.82
		Reg. t	0.91	0.87	0.83	0.95	0.90	0.83	0.62	0.80	0.75	0.88	0.84	0.90	0.82
	Scaled	Student	0.82	0.82	0.64	0.83	0.81	0.68	0.56	0.66	0.70	0.79	0.75	0.80	0.74
		Win. t	0.90	0.90	0.72	0.89	0.86	0.75	0.60	0.79	0.77	0.85	0.81	0.85	0.79
		Reg. t	0.91	0.91	0.76	0.92	0.89	0.77	0.62	0.82	0.80	0.87	0.84	0.87	0.81

We analyzed the Hugene 1.0 ST Tissue Mixture Study (Affymetrix) for differential expression, using Student t-test, Regularized t-test, and Window t-test. Summarization tests were performed on probe concentrations computed with AffyILM. Comparison between heart (mix 1) and brain (mix 9) is assumed to provide the reference list of p-values. For each combination of summarization/analysis steps (rows), Pearson's correlation coefficient has been computed on log10(p-values) between the reference analysis and several comparisons of mixtures (columns). Underlined characters highlights the top 5 correlation coefficients for each column. Raw/Scaled labels respectively refers to summarization tests performed with/without a scaling step between arrays.