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Table 1 Expression ratios of a weak and a bright spot on the same microarray, measured with three scanners at several PMT voltages

From: Profound influence of microarray scanner characteristics on gene expression ratios: analysis and procedure for correction

 

ScanArray4000 I

ScanArray4000 II

 

GenePix4000B

PMT (R/G)

Weak spot

Bright spot

Weak spot

Bright spot

PMT (R/G)

Weak spot

Bright spot

62/62*

2.28

0.74

1.88

0.60

800/700*

1.63

0.61

56/62*

2.43

0.76

1.79

0.58

700/700*

1.68

0.55

50/62

2.15

0.74

1.49

0.61

500/700

1.58

0.47

45/62

1.26

0.95

0.43

0.71

400/700

4.98

0.47

40/62

0.55

1.41

0.16

0.76

300/700

14.14

0.98

62/56*

2.25

0.76

1.93

0.62

800/500*

1.71

0.61

62/50

2.36

0.71

2.12

0.58

800/400*

1.79

0.64

62/45

3.37

0.62

3.75

0.50

800/300

1.75

0.62

62/40

92.9

0.48

-

0.41

800/200

0.10

0.46

  1. Data subjected to total intensity normalization are shown. The PMT voltages (PMT) used during scanning are shown for the red (R) and green (G) channel separately as % of maximum voltage (ScanArray4000 I and II) or voltage (GenePix4000B). The PMT voltages leading to intensities within the usable range of the scanners and, hence, reproducible ratios for all spots in the array are indicated (*).