Baseline and Threshold Setting in qPCR
The baseline is the early-cycle range used to subtract background fluorescence, and the threshold is the fluorescence level whose crossing defines Cq; both must sit in the exponential phase, above background noise and below the plateau. A baseline set too late truncates real signal and inflates Cq, while a threshold set in the plateau destroys the log-linear relationship to template amount.
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The baseline is the early-cycle range used to subtract background fluorescence, and the threshold is the fluorescence level whose crossing defines Cq; both must sit in the exponential phase, above background noise and below the plateau. A baseline set too late truncates real signal and inflates Cq, while a threshold set in the plateau destroys the log-linear relationship to template amount.
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