From hybridization theory to microarray data analysis: performance evaluation

Berger, Fabrice; Carlon, Enrico

doi:10.1186/1471-2105-12-464

BMC Bioinformatics

Table 5 Comparison of the differential expression analysis on HG-U133Plus2 arrays preprocessed with popular methods

From: From hybridization theory to microarray data analysis: performance evaluation

Method	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
MAS 5 1-Step Tukey-Biweight	Bg	Student	0.71	0.67	0.54	0.74	0.82	0.45	0.58	0.54	0.70	0.62	0.75	0.60	0.73
		Win. t	0.83	0.81	0.69	0.85	0.89	0.51	0.66	0.62	0.78	0.71	0.83	0.68	0.81
		Reg. t	0.83	0.79	0.68	0.85	0.88	0.45	0.61	0.57	0.77	0.69	0.83	0.65	0.78
	Bg	Student	0.80	0.79	0.69	0.83	0.86	0.62	0.69	0.78	0.82	0.78	0.82	0.79	0.83
	Norm	Win. t	0.89	0.88	0.79	0.90	0.92	0.66	0.73	0.84	0.88	0.84	0.88	0.84	0.88
		Reg. t	0.89	0.88	0.77	0.89	0.91	0.61	0.71	0.82	0.86	0.83	0.87	0.83	0.87
	PM	Student	0.72	0.70	0.56	0.77	0.85	0.52	0.59	0.57	0.72	0.68	0.80	0.62	0.73
		Win. t	0.82	0.82	0.72	0.87	0.93	0.59	0.69	0.66	0.80	0.77	0.88	0.68	0.80
		Reg. t	0.76	0.77	0.67	0.84	0.90	0.52	0.62	0.60	0.77	0.73	0.86	0.62	0.76
	PM	Student	0.84	0.82	0.73	0.86	0.89	0.66	0.75	0.77	0.84	0.79	0.85	0.82	0.86
	Norm	Win. t	0.91	0.90	0.83	0.92	0.94	0.69	0.79	0.82	0.88	0.85	0.91	0.86	0.91
		Reg. t	0.90	0.89	0.79	0.91	0.92	0.64	0.75	0.79	0.85	0.82	0.88	0.84	0.87
Plier	Raw	Student	0.73	0.71	0.56	0.75	0.82	0.57	0.56	0.64	0.70	0.71	0.76	0.67	0.71
		Win. t	0.82	0.80	0.70	0.83	0.87	0.60	0.63	0.67	0.74	0.76	0.82	0.70	0.77
		Reg. t	0.82	0.80	0.70	0.85	0.87	0.65	0.64	0.71	0.72	0.80	0.81	0.73	0.75
dChip Li-Wong MBEI	PM	Student	0.82	0.81	0.70	0.81	0.86	0.63	0.73	0.73	0.80	0.71	0.81	0.78	0.82
	Norm	Win. t	0.88	0.87	0.79	0.86	0.89	0.63	0.76	0.73	0.82	0.74	0.84	0.79	0.85
		Reg. t	0.88	0.86	0.73	0.85	0.88	0.58	0.73	0.70	0.78	0.70	0.81	0.77	0.81
	Norm	Student	0.80	0.79	0.72	0.80	0.84	0.59	0.71	0.74	0.80	0.73	0.81	0.74	0.80
		Win. t	0.86	0.85	0.79	0.84	0.87	0.61	0.73	0.76	0.82	0.76	0.84	0.77	0.83
		Reg. t	0.84	0.84	0.75	0.83	0.86	0.54	0.71	0.73	0.81	0.73	0.82	0.74	0.81
qFARMS	Norm	Student	0.81	0.80	0.72	0.81	0.85	0.65	0.71	0.73	0.79	0.73	0.81	0.77	0.81
		Win. t	0.85	0.84	0.73	0.81	0.84	0.54	0.64	0.69	0.77	0.70	0.79	0.71	0.78
		Reg. t	0.89	0.89	0.77	0.85	0.89	0.56	0.69	0.76	0.83	0.75	0.84	0.76	0.83
lFARMS	Norm	Student	0.81	0.79	0.70	0.79	0.84	0.62	0.64	0.72	0.73	0.72	0.78	0.76	0.80
		Win. t	0.85	0.84	0.73	0.81	0.84	0.54	0.60	0.68	0.72	0.70	0.76	0.70	0.77
		Reg. t	0.89	0.88	0.75	0.83	0.89	0.52	0.66	0.69	0.78	0.68	0.82	0.72	0.83
RMA Median-polish	Norm	Student	0.83	0.82	0.73	0.82	0.86	0.65	0.72	0.75	0.81	0.75	0.82	0.78	0.82
		Win. t	0.92	0.91	0.85	0.90	0.92	0.71	0.79	0.82	0.86	0.84	0.88	0.84	0.88
		Reg. t	0.93	0.93	0.87	0.92	0.93	0.73	0.79	0.84	0.88	0.86	0.90	0.86	0.89
GCRMA Median-polish	Raw	Student	0.85	0.84	0.76	0.83	0.89	0.57	0.72	0.49	0.78	0.61	0.84	0.69	0.83
		Win. t	0.90	0.88	0.84	0.90	0.92	0.62	0.75	0.57	0.80	0.68	0.86	0.73	0.85
		Reg. t	0.91	0.90	0.86	0.91	0.93	0.66	0.76	0.60	0.80	0.71	0.86	0.76	0.84
	Norm	Student	0.87	0.86	0.80	0.86	0.89	0.68	0.75	0.82	0.86	0.81	0.86	0.81	0.86
		Win. t	0.92	0.92	0.86	0.90	0.92	0.69	0.78	0.85	0.88	0.85	0.89	0.84	0.89
		Reg. t	0.94	0.94	0.89	0.92	0.95	0.71	0.79	0.87	0.91	0.87	0.92	0.86	0.91

We analyzed the HG-U133plus2 Tissue Mixture Study (Affymetrix) for differential expression, using Student t-test, Regularized t-test, and Window t-test. Several previously published preprocessing methods were compared. Comparison between heart (mix 1) and brain (mix 9) is assumed to provide the reference list of p-values. For each combination of preprocessing/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 highlight the top 5 correlation coefficients for each column. Raw/Norm labels refer to raw and normalized data, PM stands for PM-only and Bg refers to background correction (using MM).

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ISSN: 1471-2105

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