Table 1 Data consistency for the dataset of 2009 genes (before 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

18

10

11

11

10

9

8

9

42

11

13

11

8

6

8

7

10

23

9

9

0.1229

Aff.T2

11

7

9

8

5

7

6

36

19

15

9

10

9

5

6

7

23

9

8

0.1112

0.0893

Aff.T3

10

7

10

11

10

11

37

12

10

9

8

7

11

9

9

22

8

12

0.1548

0.1425

0.1587

Ame.T1

72

78

31

31

28

24

5

9

84

49

42

32

23

22

21

73

29

0.1656

0.1701

0.1771

0.7562

Ame.T2

78

35

34

33

22

5

8

84

40

34

36

19

22

18

63

31

0.1536

0.1521

0.1705

0.7821

0.7743

Ame.T3

28

28

28

23

5

9

87

43

38

29

19

21

20

67

28

0.1307

0.1364

0.1732

0.3176

0.3325

0.3213

Agi.T1

81

53

19

5

9

33

20

17

88

38

38

22

29

63

0.1453

0.161

0.1674

0.3281

0.3499

0.3362

0.839

Agi.T2

51

19

6

8

32

21

18

86

36

38

23

30

61

0.114

0.1358

0.1369

0.258

0.2867

0.2637

0.5895

0.6818

Agi.T3

17

4

4

31

21

16

60

31

29

17

28

45

0.5515

0.5478

0.5551

0.2755

0.3102

0.288

0.2661

0.2866

0.234

Aff.B1

16

13

25

18

16

20

17

19

40

24

21

0.048

0.0877

0.0422

0.0612

0.0603

0.0664

0.0595

0.0681

0.047

0.1045

Aff.B2

14

4

7

9

5

9

9

33

6

10

0.0667

0.0852

0.076

0.1191

0.111

0.1255

0.1132

0.1224

0.0856

0.1377

0.061

Aff.B3

8

6

8

9

7

9

40

9

12

0.1719

0.1684

0.1836

0.9171

0.9144

0.9245

0.3525

0.368

0.2932

0.3168

0.0682

0.129

Ame.B1

48

40

34

21

23

20

73

31

0.1059

0.0963

0.0801

0.5138

0.5063

0.4695

0.1445

0.1557

0.1145

0.1694

0.0754

0.0956

0.5403

Ame.B2

49

21

30

27

20

62

27

0.0871

0.0835

0.0677

0.4045

0.3361

0.4771

0.1301

0.1396

0.0864

0.1431

0.0734

0.116

0.4397

0.529

Ame.B3

16

30

34

20

58

28

0.1451

0.1614

0.178

0.3364

0.3613

0.3429

0.8965

0.9314

0.8457

0.2932

0.0646

0.1189

0.3775

0.1539

0.131

Agi.B1

37

38

23

29

62

0.0969

0.0883

0.0912

0.1982

0.176

0.1955

0.3946

0.4142

0.2584

0.1668

0.1263

0.103

0.2066

0.2835

0.3004

0.3926

Agi.B2

73

21

30

69

0.1105

0.094

0.0984

0.1985

0.1846

0.1944

0.4178

0.4358

0.3152

0.1825

0.1251

0.1221

0.2095

0.2699

0.3055

0.4334

0.8483

Agi.B3

24

33

70

0.266

0.3221

0.2698

0.2417

0.2466

0.2555

0.2324

0.2542

0.1889

0.5176

0.5015

0.6006

0.2699

0.1957

0.1976

0.2508

0.2346

0.2555

Aff

24

27

0.1522

0.1452

0.1364

0.7625

0.7245

0.78

0.2579

0.2733

0.2008

0.2616

0.0893

0.1419

0.8224

0.8208

0.771

0.2716

0.3197

0.3181

0.2772

Ame

36

0.1477

0.145

0.1552

0.3087

0.3047

0.3087

0.7209

0.7515

0.5939

0.2708

0.1204

0.1418

0.3346

0.2721

0.2744

0.7693

0.8285

0.8607

0.3045

0.3674

Agi