Skip to main content

Table 3 Comparison of the differential expression analysis on Hugene 1.0 ST arrays preprocessed with affyILM and popular summarization procedures

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

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

  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. 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.