Table 1 Comparison of different measures for each of the 3 kits assessed in this study.

cRNA yield (ug)*

54.6 ± 0.6

2

43.1 ± 2.4

3

86.3 ± 10.9

1

Reproducibility

1

2

3

Peak range cDNA product sizes (bases)

100 – 2000

1

800

3

750–2000

2

Average fragment length (bases)

100

1

125

1

100

1

Fragmentation cRNA yield (ug)*

9.2 ± 4.3

1

4.6 ± 1.2

2

4.5 ± 1.3

2

Total time labeling reaction

22.5

1

23.5

3

22.75

2

Number of steps to labeling reaction

7

1

11

2

6

1

Cost per labeling reaction

$115.00

3

$106.00

2

$95.00

1

% of Present*

38.6 ± 0.7

1

36.8 ± 5.4

2

34.7 ± 6.4

3

Scaling Factor*

16.6 ± 7.7

3

13.7 ± 1.9

1

14.0 ± 1.4

2

Median array raw intensity*

143.1 ± 8.7

2

131.6 ± 33.6

3

168.6 ± 47.0

1

Mean array raw intensity*

1042.6 ± 34.3

3

1160.7 ± 127.5

1

1104.6 ± 73.5

2

Background*

37.4 ± 3.8

1

41.8 ± 8.6

2

49.9 ± 21.9

3

Raw Q (Noise)*

1.23 ± 0.2

1

1.4 ± 0.5

2

1.7 ± 0.8

3

Number Present (P)

21099 ± 389

1

20119 ± 2962

2

18953 ± 3477

3

Number Absent (A)

32744 ± 360

3372 ± 2933

34846 ± 3461

Number Marginal (M)

832 ± 81

1

834 ± 13

2

877 ± 16

3

Average Signal (P)

2550.4 ± 125.4

3

3054.3 ± 660.8

2

3074.7 ± 451.1

1

Average Signal (A)

90.5 ± 12.5

88.8 ± 35.3

143.9 ± 42.7

Average Signal (M)

295.5 ± 36.0

279.5 ± 105.9

430.3 ± 121.6

Average CV on GC-RMA normalized signal (All 3)

15.7%

18.0%

16.0%

Average CV on GC-RMA normalized signal (Replicates only)

11.0%

1

12.1%

2

12.3%

3

β-actin/GAPDH ratios

1

1

1

rRNA signal

1

3

2

30

41

40