Table 2 Data consistency for the dataset of 537 genes (after data filtering). The pair-wise log ratio correlation squared (LRr², lower triangle) and the percentage of overlapping genes (POG, upper triangle) are listed. T1, T2, and T3 are technical replicates; B1, B2, and B3 are biological replicates. The last three rows/columns (Affymetrix (Aff), Amersham (Ame), and Agilent (Agi)) represent results from the average of the three biological replicates. Gene selection was based on fold-change ranking, and a total of 100 genes (50 genes from each regulation direction) were selected for each comparison. Black bold numbers represent intra-platform technical or biological consistency, or cross-platform concordance.

Aff.T1

53

56

52

49

52

50

53

54

71

46

41

53

42

46

52

45

44

58

52

52

0.5745

Aff.T2

44

51

53

51

48

47

46

70

46

45

53

41

41

47

43

43

61

48

47

0.5902

0.4525

Aff.T3

52

51

52

53

54

53

69

37

37

53

36

39

53

38

37

48

46

47

0.5341

0.53

0.572

Ame.T1

88

90

58

60

54

60

39

38

95

55

52

60

37

38

53

76

50

0.5439

0.537

0.5836

0.9347

Ame.T2

89

56

58

52

59

40

39

92

57

51

58

36

36

55

77

48

0.5486

0.5499

0.5768

0.9374

0.9482

Ame.T3

57

59

53

59

40

40

94

55

54

58

36

37

55

78

48

0.4382

0.446

0.5163

0.564

0.5705

0.572

Agi.T1

89

78

57

33

40

59

35

37

89

44

50

50

49

69

0.4676

0.4847

0.5405

0.5954

0.6009

0.6052

0.9613

Agi.T2

84

57

38

42

62

39

39

93

49

55

53

50

75

0.4553

0.4617

0.5177

0.5687

0.5729

0.5796

0.9041

0.9419

Agi.T3

56

38

40

55

36

38

88

47

52

50

46

74

0.858

0.8009

0.8076

0.664

0.6755

0.68

0.5682

0.6059

0.5822

Aff.B1

41

44

60

44

47

57

45

47

64

55

55

0.4191

0.4626

0.361

0.3498

0.3524

0.3606

0.3054

0.334

0.3301

0.5029

Aff.B2

41

41

47

53

36

54

52

58

46

47

0.3238

0.417

0.2726

0.3576

0.3766

0.3844

0.3515

0.3834

0.3774

0.4083

0.4451

Aff.B3

40

38

43

41

44

47

74

46

48

0.5534

0.5502

0.5894

0.9767

0.9807

0.9818

0.5806

0.6129

0.5856

0.6871

0.3616

0.3806

Ame.B1

56

53

61

37

38

55

78

50

0.4268

0.3686

0.3707

0.6163

0.6253

0.6093

0.313

0.3422

0.3289

0.4719

0.4917

0.2973

0.6297

Ame.B2

71

37

48

46

48

72

43

0.4137

0.371

0.3575

0.579

0.5647

0.6168

0.3084

0.3389

0.3244

0.4624

0.5056

0.3427

0.5989

0.7859

Ame.B3

37

55

53

52

70

50

0.4634

0.4739

0.5363

0.5885

0.594

0.5982

0.977

0.9889

0.9686

0.5979

0.3298

0.3784

0.6059

0.3348

0.3306

Agi.B1

47

52

51

50

74

0.3926

0.3393

0.3296

0.3591

0.3581

0.3627

0.4694

0.5186

0.5031

0.4293

0.5678

0.3239

0.3674

0.5783

0.5682

0.5072

Agi.B2

85

53

45

72

0.3888

0.3461

0.332

0.355

0.359

0.3598

0.4975

0.541

0.5335

0.4318

0.5659

0.353

0.3654

0.5435

0.5677

0.5349

0.9525

Agi.B3

53

46

78

0.6397

0.694

0.5684

0.5686

0.5842

0.5934

0.5141

0.5563

0.5432

0.7705

0.7688

0.7978

0.5942

0.5167

0.5437

0.5491

0.5396

0.5566

Aff

58

58

0.5379

0.4995

0.5108

0.842

0.8412

0.856

0.4661

0.5019

0.4805

0.6277

0.5041

0.3921

0.8639

0.8909

0.8765

0.4931

0.5547

0.5425

0.6341

Ame

51

0.4877

0.4581

0.4759

0.5176

0.5212

0.5249

0.7747

0.816

0.7989

0.5766

0.5354

0.4123

0.532

0.5341

0.5366

0.8137

0.8863

0.9037

0.6372

0.6098

Agi