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Table 4 Summary of values of the coefficients of standard deviation function and K α coefficients

From: Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution

GeneChip/average/SD/CV

No. of probe sets

Cons. samp. size

No. of arrays

No. of comp.

Coefficient. of st. dev. function

Average Kalpha values in given probability intervals

     

a1

a2

0.500

0.600

0.700

0.800

0.900

0.950

0.990

0.995

Total average [sum]

  

[682]

[900]

9.66

0.266

0.642

0.808

1.009

1.275

1.711

2.145

3.226

3.741

Total SD

    

9.99

0.146

0.033

0.039

0.043

0.045

0.052

0.080

0.270

0.390

Total CV

    

1.03

0.550

0.052

0.049

0.043

0.035

0.030

0.037

0.084

0.104

HuGeneFL [a1]

7070

12

11

54

8.61

0.115

0.64

0.81

1.01

1.27

1.71

2.16

3.41

4.09

HuGeneFL [b]

7070

12

13

78

8.09

0.418

0.61

0.77

0.97

1.24

1.73

2.24

3.58

4.18

HuGeneFL [c]

7070

25

5

10

34.58

0.435

0.61

0.76

0.94

1.20

1.60

2.03

3.39

4.10

HuGeneFL [c]

7070

25

5

10

28.93

0.393

0.59

0.73

0.92

1.18

1.60

2.07

3.42

4.07

HuGeneFL avg [sum]

  

[34]

[152]

20.05

0.34

0.61

0.77

0.96

1.22

1.66

2.13

3.45

4.11

HuGeneFL SD

    

13.71

0.15

0.02

0.03

0.04

0.04

0.07

0.10

0.09

0.05

HuGeneFL CV

    

0.68

0.44

0.04

0.04

0.04

0.04

0.04

0.05

0.03

0.01

HG-U95Av2 [d]

12559

12

5

10

6.30

0.688

0.61

0.78

1.00

1.30

1.83

2.32

2.98

3.26

HG-U95Av2 [e1]

12559

25

15

15

10.49

0.199

0.65

0.82

1.01

1.27

1.68

2.07

3.05

3.55

HG-U95Av2 [e2]

12559

25

15

15

10.59

0.200

0.64

0.81

1.01

1.26

1.67

2.07

3.07

3.56

HG-U95Av2 [e3]

12559

25

15

15

10.41

0.189

0.63

0.80

1.00

1.25

1.66

2.07

3.06

3.55

HG-U95Av2 [e4]

12559

25

12

12

10.91

0.185

0.63

0.79

0.99

1.24

1.66

2.04

3.02

3.50

HG-U95Av2 [e5]

12559

25

4

2

6.50

0.394

0.65

0.82

1.01

1.26

1.65

2.05

3.05

3.62

HG-U95Av2 [f]

12559

25

4

2

5.64

0.155

0.64

0.81

1.00

1.25

1.66

2.04

2.92

3.31

HG-U95Av2 [g1]

12559

25

2

1

4.79

0.479

0.61

0.76

0.95

1.20

1.64

2.10

3.22

3.71

HG-U95Av2 [g1]

12559

25

5

10

3.31

0.500

0.64

0.80

1.00

1.26

1.69

2.09

2.98

3.29

HG-U95Av2 avg [sum]

  

[77]

[82]

7.66

0.33

0.63

0.80

1.00

1.26

1.68

2.09

3.04

3.48

HG-U95Av2 SD

    

2.94

0.19

0.02

0.02

0.02

0.03

0.06

0.09

0.08

0.16

HG-U95Av2 CV

    

0.38

0.57

0.02

0.02

0.02

0.02

0.04

0.04

0.03

0.05

HG-U95B [d]

12563

12

5

10

16.26

0.636

0.63

0.80

1.01

1.30

1.80

2.28

3.18

3.68

HG-U95B [e5]

12563

25

2

1

17.95

0.167

0.64

0.80

0.99

1.24

1.65

2.02

3.08

3.54

HG-U95C [d]

12587

12

5

10

20.57

0.603

0.64

0.81

1.02

1.30

1.77

2.25

3.39

3.98

HG-U95C [e5]

12587

25

2

1

16.42

0.178

0.63

0.79

0.99

1.23

1.62

2.00

3.06

3.61

HG-U95D [d]

12587

12

5

10

39.79

0.501

0.62

0.78

0.99

1.28

1.77

2.33

3.80

4.42

HG-U95D [e5]

12587

25

2

1

54.45

0.240

0.63

0.79

0.99

1.23

1.62

2.05

2.98

3.48

HG-U95E [d]

12582

12

5

10

31.84

0.534

0.60

0.76

0.97

1.27

1.78

2.29

3.53

4.08

HG-U95E [e5]

12582

25

2

1

45.64

0.215

0.63

0.79

1.00

1.25

1.64

2.02

2.88

3.31

HG-U95B to E avg [sum]

  

[28]

[44]

30.37

0.38

0.63

0.79

0.99

1.26

1.71

2.16

3.24

3.76

HG-U95B to E SD

    

14.87

0.20

0.01

0.01

0.02

0.03

0.08

0.14

0.31

0.37

HG-U95B to E CV

    

0.49

0.53

0.02

0.02

0.02

0.02

0.05

0.07

0.10

0.10

HG-U133A 2.0 [e6]

22225

25

15

15

4.55

0.091

0.65

0.82

1.02

1.28

1.72

2.14

3.14

3.62

HG-U133A 2.0 [e7]

22225

25

15

15

4.50

0.106

0.66

0.84

1.04

1.31

1.75

2.17

3.18

3.63

HG-U133A 2.0 [e8]

22225

25

12

12

4.10

0.108

0.67

0.84

1.05

1.32

1.77

2.21

3.26

3.75

HG-U133A 2.0 [h1]

22225

25

8

4

3.91

0.288

0.64

0.80

1.00

1.26

1.67

2.08

3.05

3.54

HG-U133A 2.0 [i1]

22225

12

4

6

6.25

0.210

0.65

0.82

1.01

1.27

1.68

2.08

3.04

3.48

HG-U133A 2.0 [j]

22225

25

5

10

6.54

0.390

0.62

0.79

0.98

1.25

1.68

2.10

3.13

3.62

HG-U133A 2.0 [j]

22225

25

5

10

5.54

0.393

0.62

0.79

0.98

1.25

1.66

2.08

3.10

3.64

HG-U133A 2.0 [k1]

22225

25

6

15

3.68

0.672

0.63

0.80

1.00

1.27

1.71

2.11

2.84

3.16

HG-U133A 2.0 [k1]

22225

25

3

3

4.95

0.435

0.59

0.74

0.93

1.19

1.65

2.15

3.37

3.79

HG-U133A 2.0 [l1]

22225

25

6

3

6.45

0.151

0.64

0.81

1.01

1.27

1.68

2.08

3.06

3.55

HG-U133A 2.0 [l2]

22225

25

12

6

6.78

0.148

0.65

0.82

1.02

1.27

1.67

2.06

2.93

3.33

HG-U133A 2.0 avg [sum]

  

[91]

[99]

5.21

0.27

0.64

0.80

1.00

1.27

1.69

2.11

3.10

3.56

HG-U133A 2.0 SD

    

1.15

0.18

0.02

0.03

0.03

0.03

0.04

0.05

0.15

0.18

HG-U133A 2.0 CV

    

0.22

0.67

0.03

0.03

0.03

0.03

0.02

0.02

0.05

0.05

HG-U133 Plus 2 [i2]

54000

50

8

10

3.94

0.188

0.68

0.85

1.06

1.33

1.76

2.17

3.11

3.55

HG-U133 Plus 2 [l3]

54000

50

20

27

4.03

0.086

0.65

0.82

1.02

1.28

1.69

2.07

2.95

3.34

HG-U133 Plus 2 avg [sum]

  

[28]

[37]

3.99

0.14

0.67

0.83

1.04

1.30

1.72

2.12

3.03

3.44

HG-Focus [k2]

8756

12

9

36

4.13

0.216

0.70

0.87

1.08

1.35

1.76

2.15

3.06

3.47

HG-Focus [k2]

8756

12

4

6

4.13

0.181

0.68

0.86

1.07

1.33

1.76

2.18

3.08

3.56

HG-Focus [k2]

8756

12

4

6

3.90

0.198

0.70

0.87

1.08

1.36

1.81

2.22

3.15

3.55

HG-Focus [k2]

8756

12

4

6

3.69

0.176

0.68

0.86

1.07

1.35

1.79

2.19

3.17

3.64

HG-Focus [k2]

8756

12

5

10

3.46

0.183

0.67

0.85

1.05

1.33

1.77

2.19

3.12

3.49

HG-Focus [k2]

8756

12

4

6

4.01

0.205

0.71

0.89

1.10

1.38

1.81

2.19

3.11

3.53

HG-Focus [k2]

8756

12

4

6

3.98

0.174

0.68

0.85

1.06

1.32

1.74

2.14

3.06

3.43

HG-Focus avg [sum]

  

[34]

[76]

3.90

0.19

0.69

0.86

1.07

1.35

1.78

2.18

3.11

3.52

HG-Focus SD

    

0.24

0.02

0.01

0.02

0.02

0.02

0.03

0.03

0.04

0.07

HG-Focus CV

    

0.06

0.08

0.02

0.02

0.01

0.01

0.01

0.01

0.01

0.02

MG-Mu11kSubA, SubB [a]

13069

12

10

20

9.98

0.121

0.59

0.75

0.95

1.22

1.70

2.20

3.65

4.48

MG-Mu11kSubA, SubB [a]

13069

12

10

20

8.03

0.170

0.59

0.74

0.94

1.20

1.68

2.19

3.78

4.66

MG-Mu11kSubA, SubB [a]

13069

12

10

20

8.21

0.145

0.60

0.76

0.96

1.23

1.70

2.21

3.70

4.52

MG-Mu11kSubA, SubB [a]

13069

12

10

20

5.32

0.139

0.56

0.71

0.91

1.19

1.71

2.30

4.03

4.84

MG-Mu11kSubA, SubB [m1]

13069

12

8

4

13.86

0.321

0.64

0.81

1.01

1.28

1.73

2.22

3.62

4.24

MG Mu11kSubA, SubB [n1]

13069

12

20

10

11.84

0.420

0.66

0.82

1.01

1.26

1.71

2.21

3.61

4.32

MG-Mu11kSubA, SubB avg [sum]

  

[68]

[94]

9.54

0.219

0.61

0.77

0.96

1.23

1.70

2.22

3.73

4.51

MG-Mu11kSubA, SubB SD

    

3.03

0.122

0.04

0.04

0.04

0.04

0.02

0.04

0.16

0.22

MG-Mu11kSubA, SubB CV

    

0.32

0.557

0.06

0.05

0.04

0.03

0.01

0.02

0.04

0.05

Mu19kSubA, B, C [m2]

12420

12

12

6

15.41

0.314

0.63

0.79

0.99

1.25

1.73

2.26

3.95

4.56

MG-U74Av2 [o]

12588

12

6

6

8.72

0.180

0.59

0.75

0.95

1.23

1.70

2.20

3.56

4.30

MG-U74Av2 [o]

12588

12

5

4

6.97

0.230

0.58

0.74

0.94

1.23

1.71

2.24

3.68

4.48

MG-U74Av2 [p]

12588

12

7

21

9.50

0.125

0.59

0.75

0.95

1.24

1.72

2.21

3.54

4.30

MG-U74Av2 [q]

12588

12

5

4

4.97

0.229

0.68

0.85

1.06

1.33

1.76

2.19

3.23

3.76

MG-U74Av2 [l4]

12588

12

9

9

7.50

0.111

0.67

0.83

1.03

1.30

1.73

2.13

3.09

3.53

MG-U74Av2 [r]

12588

12

10

20

4.69

0.269

0.65

0.82

1.02

1.29

1.73

2.17

3.31

3.89

MG-U74Av2 [r]

12588

12

3

3

3.30

0.238

0.64

0.80

1.00

1.27

1.71

2.17

3.48

4.04

MG-U74Av2 [e5]

12588

12

2

1

3.83

0.184

0.64

0.81

1.00

1.27

1.69

2.10

3.15

3.80

MG-U74Av2 [g2]

12588

12

2

1

13.50

0.451

0.64

0.81

1.01

1.27

1.72

2.16

3.36

3.95

MG U74Av2 [n2]

12400

12

26

13

6.56

0.113

0.64

0.80

1.00

1.27

1.70

2.12

3.15

3.67

MG-U74Av2 avg [sum]

  

[75]

[82]

6.96

0.213

0.63

0.80

1.00

1.27

1.72

2.17

3.36

3.97

MG-U74Av2 SD

    

3.07

0.101

0.03

0.04

0.04

0.03

0.02

0.04

0.20

0.31

MG-U74Av2 CV

    

0.44

0.472

0.06

0.05

0.04

0.02

0.01

0.02

0.06

0.08

MG-U430A [l5]

22636

25

10

5

7.68

0.132

0.65

0.81

1.01

1.27

1.68

2.06

2.94

3.36

MG-U430A [l6]

22636

25

5

10

10.08

0.265

0.67

0.84

1.04

1.30

1.71

2.10

2.98

3.35

MG-U430A [l6]

22636

25

5

10

9.44

0.160

0.65

0.81

1.01

1.27

1.67

2.05

2.93

3.30

MG-U430A

  

[20]

[25]

9.07

0.186

0.65

0.82

1.02

1.28

1.69

2.07

2.95

3.34

MG-U430A

    

1.24

0.070

0.01

0.02

0.02

0.02

0.02

0.03

0.03

0.03

MG-U430A

    

0.14

0.377

0.02

0.02

0.02

0.02

0.01

0.01

0.01

0.01

RG-U34A [h2]

8740

12

35

34

1.82

0.316

0.64

0.81

1.01

1.28

1.73

2.21

3.40

3.95

RG-U34A [l7]

8740

12

6

3

3.25

0.226

0.68

0.85

1.06

1.33

1.76

2.17

3.20

3.77

RG-U34A, [l8]

8740

12

4

2

6.01

0.146

0.65

0.83

1.03

1.29

1.72

2.11

3.10

3.60

RG-U34A avg [sum]

  

[45]

[39]

3.70

0.229

0.66

0.83

1.03

1.30

1.74

2.16

3.24

3.78

RG-U34A SD

    

2.13

0.085

0.02

0.02

0.02

0.02

0.02

0.05

0.15

0.17

RG-U34A CV

    

0.58

0.371

0.03

0.03

0.02

0.02

0.01

0.02

0.05

0.05

RT-U34 Neurobiology [l7]

982

12

40

20

1.77

0.194

0.60

0.75

0.96

1.22

1.65

2.08

3.12

3.38

Drosophila [s]

13976

12

6

6

2.20

0.081

0.66

0.83

1.04

1.31

1.73

2.17

3.21

3.67

E. coli [t]

7290

12

38

39

3.09

0.337

0.65

0.83

1.04

1.32

1.78

2.24

3.45

4.03

E. coli [u]

7290

12

15

30

1.88

0.302

0.65

0.83

1.04

1.34

1.81

2.29

3.47

4.04

E. Coli avg [sum]

  

[53]

[69]

2.23

0.228

0.64

0.81

1.02

1.30

1.74

2.19

3.31

3.78

ATH1 [v1]

22700

25

14

17

9.22

0.307

0.68

0.85

1.05

1.31

1.71

2.09

2.95

3.31

ATH1 [v1]

22700

25

34

36

11.18

0.269

0.68

0.85

1.05

1.31

1.71

2.08

2.91

3.26

ATH1 [w]

22700

25

8

4

6.26

0.279

0.65

0.81

1.01

1.27

1.69

2.10

3.06

3.45

ATH1 [x]

22700

25

4

2

3.09

0.232

0.68

0.85

1.05

1.31

1.72

2.12

3.17

3.70

ATH1 [y]

22700

25

4

2

3.07

0.247

0.66

0.82

1.02

1.28

1.68

2.08

3.09

3.60

ATH1 avg [sum]

  

[64]

[61]

6.57

0.267

0.67

0.84

1.04

1.30

1.70

2.09

3.03

3.46

ATH1 SD

    

3.63

0.029

0.01

0.02

0.02

0.02

0.02

0.02

0.11

0.19

ATH1 CV

    

0.55

0.108

0.02

0.02

0.02

0.02

0.01

0.01

0.03

0.05

Arabidopsis [v2]

8200

12

7

8

7.69

0.403

0.75

0.94

1.14

1.40

1.79

2.15

2.89

3.18

  1. No. of probe sets is approximate number of the probe sets on array, Cons. samp. size is number of the probe pairs in a consecutive sample, No. of arrays is a number of arrays tested, No. of comp. is the number of pair-wise comparisons among the replicates, coefficients a1 and a2 are the coefficients of standard deviation function and Kalpha is the coefficient determining probability interval; "h." stands for "human," "m." for "murine." Average values, sum of arrays and comparisons (in square brackets), standard deviations (SD) and coefficients of variation (CV) of each GeneChip type are printed in bold italics.
  2. Data sources:
  3. a1 – J. P. Novak et al., HuGeneFl, IMR90 human cell line [10].
  4. a2 – J. P. Novak et al., HuGeneFl, mouse tissues, adult male C57BL/6 [10].
  5. b – A.-M. Mes-Masson, P. Tonin and coworkers, HuGeneFL, normal ovarian surface epithelial (NOSE) primary cell cultures, private communication.
  6. c – P. Permana, HuGeneFL, human skeletal muscle tissue [35].
  7. d – P. Tonin and A.-M. Mes-Masson and coworkers, HG-U95A to E, epithelial ovarian cancer (EOC) cell line [36].
  8. e1 – Affymetrix, HG-U95A, latin square, experiments 1 to 5.
  9. e2 – Affymetrix, HG-U95A, latin square, experiments 6 to 10.
  10. e3 – Affymetrix, HG-U95A, latin square experiments 11 to 15.
  11. e4 – Affymetrix, HG-U95A, latin square, experiments 16 to 19.
  12. e5 – Affymetrix, HG-U95A to E, Demo Data.
  13. e6 – Affymetrix, HG-U133A, latin square, experiments 1 to 5.
  14. e7 – Affymetrix, HG-U133A, latin square, experiments 6 to 10.
  15. e8 – Affymetrix, HG-U133A, latin square, experiments 11 to 14.
  16. f – M. S. Rolph, HG-U95Av2, primary human bronchial epithelial cells.
  17. g1 – Z. Gatalica, HG-U95Av2, breast tumor tissues and normal breast tissue samples [37].
  18. g2 – Z. Gatalica, MG-U74Av2, mouse kidney tissue.
  19. h1 – M. Boerma, HG-U133A 2.0, primary human umbilical vein endothelial cells (HUVECs) and the immortalized HUVEC cell line EA.hy926 [38].
  20. h2 – M. Boerma, RG-U34A, cultures enriched for neonatal rat cardiac myocytes or fibroblasts [39].
  21. i1 – M. Hajduch, HG-U133A 2.0.
  22. i2 – M. Hajduch, HG-U133 plus 2.
  23. j – S. Y. Kim and D. J. Volsky, HG-U133A 2.0, human fetal astrocytes, normal and pseudotyped HIV-1 infected [40].
  24. k1 – O. Modlich, HG-U133A 2.0, human superficial and invasive bladder tumors [41].
  25. k2 – O. Modlich and Raschke, Focus arrays, human lymphoma cell line Kaspas-422, DSMZ no.: ACC 32 (follicular B cell).
  26. l1 – C. Wang and J. Xu, HG-U133A 2.0, human lymphoblast cell line.
  27. l2 – C. Wang and J. Xu, HG-U133A 2.0, human pancreatic islet.
  28. l3 – C. Wang and J. Xu, HG-U133 Plus 2, Stratagene Universal Human Reference RNA, Ambion Human Brain Reference RNA and mixtures of both in different concentrations.
  29. l4 – C. Wang and J. Xu, MG-U74Av2, mouse biliary epithelial cells.
  30. l5 – C. Wang and J. Xu, MG-U430A, mouse spleen.
  31. l6 – C. Wang and J. Xu, MG-U430A, myofibroblast cell line.
  32. l7 – C. Wang and J. Xu, RG-U34A, rat livers.
  33. l8 – C. Wang and J. Xu, RG-U34A, rat bone marrow stem cells.
  34. m1 – McInnes and coworkers, MG-Mu11kSubA, SubB, retinal RNA samples from WT and Rom1 knock-out mice [36].
  35. m2 – McInnes, Szego and coworkers, MG-Mu19kSubA, SubB, SubC, retinal RNA samples from WT and Rom1 knock-out mice [42].
  36. n1 – Burton, McGehee and coworkers, MG-Mu11kSubA, SubB, 3T3-L1 adipocytes [43].
  37. n2 – Burton, McGehee and coworkers, MG-U74Av2,3T3-L1 adipocyte cultures [44].
  38. o – M. Cosio, MG-U74Av2, lung tissues, murine strains NZW and AKR.
  39. p – R. St-Arnaud, MG-U74Av2, C2C12 cells [45].
  40. q – J. Hidalgo, MG-U74Av2, cortex samples, C57B6 normal and IL6 KO mice [46].
  41. r – D. Radzioch, C. Guilbault and coworkers, MG-U74Av2, C57BL/6 (B6) WT and C57BL/6-Cftr-/- (KO) inbred mice [15].
  42. s – S. E. Choe, Drosophila, Drosophila Gene Collection release 1.0 cDNA clones [19].
  43. t – F. Blattner, E. coli antisense genome, E. coli K-12 strain MG1655 and an isogenic fnr::Spr Smr strain [47].
  44. u – J. Slonczewski and S. BonDurant, E. coli antisense genome, E. coli K-12 strain W3110 [48].
  45. v1 – E. Blumwald and J. Sottosanto, ATH1, A. thaliana ecotype Wassilewskija, wild-type line (WS), nhx1 'knockout' line, and a knockout restoration line; [49] and unpublished data.
  46. v2 – E. Blumwald and J. Sottosanto, arabidopsis, A. thaliana ecotype Wassilewskija, wild-type line (WS), and a nhx1 'knockout' line (unpublished data).
  47. w – D. Honys and D. Twell, ATH1, Arabidopsis thaliana ecotype Landsberg erecta plants [50].
  48. x – E. Nambara and K. Nakabayashi, ATH1, Arabidopsis thaliana (L.) Heynh of ecotype Columbia [51].
  49. y – E. Nambara and K. Tatematsu, ATH1, Arabidopsis thaliana (L.) Heynh of ecotype Columbia [52].