Table 1

Comparison of different measures for each of the 3 kits assessed in this study.
Stage
 Parameters
 One Cycle
 Rank
 BioArray
 Rank
 Superscript
 Rank
Labeling Protocol
 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
Signal measures
 % 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
Internal Control genes
 β-actin/GAPDH ratios
1
1
1

rRNA signal
1
3
2
Total score

30
41
40

Several criteria were evaluated for each stage in the generation of labeled target and each afforded a score relative to performance 1 = good, 3 = worst.

Lonergan et al. BMC Biotechnology 2007 7:24   doi:10.1186/1472-6750-7-24