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Table 1 GeneChip Array performance metrics

From: Gene expression profiling of whole blood: Comparison of target preparation methods for accurate and reproducible microarray analysis

Sample Bg % P Mean Signal Actin Intensity Actin 3'/5' Ratio GAPDH Intensity GAPDH 3'/5' Ratio
METHOD 1        
A 54.3 48.3% 95.5 751.4 7.6 410.4 5.9
C 50.3 53.1% 123.3 3437.5 1.4 988.1 1.8
D 47.8 52.2% 107.5 3692.0 1.1 1216.7 1.1
A frozen 49.0 51.2% 95.0 2641.6 1.4 1073.3 1.2
C frozen 48.7 54.0% 117.7 3618.0 1.2 1324.7 1.2
D frozen 49.7 51.3% 98.6 2933.7 1.1 1005.6 1.5
Average* 50.1 52.4% 106.3 2845.7 1.2 1003.1 1.4
METHOD 2        
A 58.2 58.9% 270.4 8145.6 1.5 3492.0 0.9
C 52.7 58.7% 220.0 6812.9 1.5 2742.4 1.0
D 62.2 55.9% 179.7 6953.0 1.1 2697.9 1.0
A frozen 53.1 57.2% 177.2 5616.2 1.5 2336.8 1.1
C frozen 56.1 58.5% 195.4 6458.0 1.2 2580.7 0.9
D frozen 55.2 58.3% 196.8 6952.1 1.2 3016.1 1.0
Average 56.2 57.9% 206.6 6823.0 1.3 2811.0 1.0
METHOD 3        
A 53.2 56.9% 155.8 2014.2 3.2 680.1 8.3
C 51.3 56.1% 145.1 4514.5 1.1 689.9 4.3
D 51.7 55.7% 144.5 3492.7 1.7 676.4 8.0
A frozen 46.5 56.6% 136.7 3400.5 2.0 1442.0 1.4
C frozen 49.5 55.1% 129.7 1491.0 3.9 583.8 8.9
D frozen 45.6 56.3% 132.2 3598.3 1.2 678.7 2.9
Average 49.6 56.1% 140.7 3085.2 2.2 791.8 5.6
METHOD 4        
A 41.8 55.8% 97.0 2057.3 7.2 301.5 1.5
C 30.9 53.4% 63.6 1658.4 10.7 161.3 1.6
D 31.2 55.7% 82.4 2039.6 10.2 259.4 1.9
A frozen 30.8 53.8% 65.2 1577.0 15.5 183.4 2.9
C frozen 34.8 53.3% 73.2 1753.5 11.1 190.2 2.1
D frozen 37.9 53.3% 79.3 1838.4 10.6 256.3 1.8
Average 34.6 54.2% 76.8 1820.7 10.9 225.4 2.0
  1. Microarray targets prepared from donors A, C, and D were hybridized to the GeneChip Human Focus Array. Overall performance values determined with unscaled MAS 5.0 analysis of each array are listed. Bold font indicates metric values that fall below empirical quality control standards established in our laboratory. All arrays passed post-hybridization visual inspection. *Average values for Method 1 do not include sample A which was flagged as a low performance outlier.