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

From: Comparison of target labeling methods for use with Affymetrix GeneChips

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
  1. 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.