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Table 2 Percentage of genes identical among all genes detected by different combinations of normalization and statistical analysis

From: Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis

 

Invariant feature; AD, F

Invariant feature; AD, KW

Invariant feature; AD, SAM

Invariant feature; MBEV, F

Invariant feature; MBEV, KW

Invariant feature; MBEV, SAM

Invariant set; F

Invariant set; KW

Invariant set; SAM

Global scaling; F

Global scaling; KW

Global scaling; SAM

Invariant feature; AD, F

 

93

100

78

83

92

81

83

88

64

74

78

Invariant feature; AD, KW

74

 

95

67

79

82

74

79

81

55

67

69

Invariant feature; AD, SAM

56

66

 

51

59

74

58

61

66

41

50

54

Invariant feature; MBEV, F

69

75

82

 

96

100

77

80

82

58

67

70

Invariant feature; MBEV, KW

62

74

79

80

 

95

71

75

77

51

62

64

Invariant feature; MBEV, SAM

56

63

81

68

77

 

63

66

70

44

53

57

Invariant set; F

59

69

77

63

70

76

 

98

100

56

67

70

Invariant set; KW

56

67

74

60

68

74

90

 

96

52

66

66

Invariant set; SAM

55

64

74

58

65

73

85

89

 

49

61

66

Global scaling; F

80

87

92

81

86

90

95*

96*

98*

 

100

100

Global scaling; KW

72

83

88

73

82

85

89

96*

95*

78

 

93

Global scaling; SAM

70

78

88

71

77

84

85

89

94*

72

86

 
  1. Percentages are relative to the method defined in the column headings. Values of 100% and greater than 90% are highlighted in bold. *Percentage of genes identified after invariant probe set normalization that are also identified after global scaling (see text for details).