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Table 6 Comparison of the differential expression analysis on Hugene 1.0 ST arrays preprocessed with several popular algorithms

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

PM

Student

0.72

0.74

0.61

0.83

0.83

0.67

0.54

0.61

0.65

0.73

0.72

0.75

0.74

  

Win. t

0.82

0.82

0.69

0.89

0.86

0.70

0.57

0.71

0.69

0.80

0.77

0.80

0.77

  

Reg. t

0.79

0.81

0.64

0.87

0.83

0.65

0.56

0.67

0.69

0.78

0.77

0.76

0.72

 

PM

Student

0.80

0.80

0.65

0.88

0.83

0.71

0.60

0.83

0.79

0.84

0.80

0.81

0.78

 

Norm

Win. t

0.85

0.85

0.69

0.90

0.86

0.71

0.59

0.85

0.81

0.86

0.83

0.84

0.79

  

Reg. t

0.86

0.85

0.65

0.90

0.84

0.67

0.57

0.83

0.80

0.85

0.82

0.82

0.75

Plier

Raw

Student

0.86

0.74

0.75

0.90

0.85

0.78

0.52

0.74

0.71

0.83

0.77

0.85

0.80

  

Win. t

0.90

0.83

0.79

0.92

0.89

0.80

0.59

0.77

0.74

0.85

0.81

0.87

0.82

  

Reg. t

0.91

0.84

0.81

0.94

0.89

0.83

0.60

0.79

0.74

0.87

0.82

0.89

0.82

dChip Li-Wong MBEI

PM

Student

0.80

0.74

0.65

0.86

0.84

0.71

0.49

0.63

0.71

0.77

0.77

0.79

0.77

 

Norm

Win. t

0.85

0.80

0.71

0.88

0.86

0.72

0.54

0.69

0.73

0.81

0.81

0.81

0.78

  

Reg. t

0.82

0.79

0.65

0.88

0.84

0.70

0.53

0.64

0.75

0.80

0.82

0.80

0.73

RMA Median-polish

Norm

Student

0.83

0.83

0.70

0.86

0.83

0.72

0.60

0.80

0.78

0.81

0.78

0.81

0.77

  

Win. t

0.89

0.88

0.75

0.88

0.86

0.73

0.60

0.83

0.80

0.84

0.81

0.83

0.79

  

Reg. t

0.93

0.92

0.80

0.93

0.90

0.77

0.63

0.87

0.84

0.89

0.85

0.88

0.84

GCRMA Median-polish

Raw

Student

0.84

0.86

0.76

0.82

0.88

0.53

0.64

0.41

0.69

0.75

0.76

0.69

0.81

  

Win. t

0.87

0.89

0.79

0.86

0.87

0.56

0.60

0.49

0.68

0.80

0.75

0.73

0.79

  

Reg. t

0.90

0.91

0.84

0.88

0.90

0.65

0.62

0.44

0.70

0.84

0.77

0.74

0.82

 

Norm

Student

0.85

0.85

0.78

0.89

0.86

0.71

0.68

0.83

0.82

0.84

0.82

0.80

0.80

  

Win. t

0.89

0.88

0.80

0.89

0.86

0.70

0.62

0.84

0.80

0.84

0.81

0.82

0.79

  

Reg. t

0.94

0.94

0.86

0.95

0.92

0.75

0.66

0.89

0.86

0.90

0.86

0.88

0.84

  1. 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. Several previously published preprocessing methods were tested. 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 highlights the top 5 correlation coefficients for each column. Raw/Norm labels refer to raw and normalized data, PM stands for PM-only methods.