A sample will flag (not pass the quality control) if Incubation Control 2 or Detection Control (corresponding to that specific sample) deviates more than a pre-determined value (+/- 0.3) from the median value of all samples on the plate.
Flags may occur due to operator error, for example, or because of the properties/quality of a specific sample. Flagged samples due to operator error are always rerun at Analysis Service. Samples that flag due to sample quality/ properties are included in the data set but should be handled with care.
If more than 1/6 of the samples per run are flagged, there is a high probability that the entire run is unreliable and should be disregarded and rerun.