Agilent CGH QC Metric

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Each Agilent text extract file contains QC metric columns. Agilent QC metric values are imported as a part of design in the ArrayStudio OmicData. User can filter samples based on these QC values in observation filter tab.

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According to the Agilent Feature Extraction Software (v10.7) User Guide, page 93, thresholds to call Good/Excellent are below:

Excellent Good Evaluate
Metric_IsGoodGrid >1 NA <1
Metric_AnyColorPrcntFeatNonUnifOL <1 1 to 5 >5
Metric_DerivativeLR_Spread <0.20 0.20 to 0.30 >0.30
Metric_gRepro 0 to 0.05 0.05 to 0.20 <0 or >0.20
Metric_g_BGNoise <5 5 to 10 >10
Metric_g_Signal2Noise >100 30 to 100 <30
Metric_g_SignalIntensity >150 50 to 150 <50
Metric_rRepro 0 to 0.05 0.05 to 0.20 <0 or >0.20
Metric_r_BGNoise <5 5 to 10 >10
Metric_r_Signal2Noise >100 30 to 100 <30
Metric_r_SignalIntensity >150 50 to 150 <50

g is for green and r is for red. Please check Agilent documents for the detail description for each metric. They are generated by the feature extraction software.