Flag bad technical replicates based on a standard deviation threshold
qbase+ flags bad replicates based on a user defined maximum allowed difference in Cq values (defined in the Experiment quality control settings).
There is a relation between the standard deviation and difference in Cq (independent of the actual Cq values). In fact, the standard deviation increases 0.1 units per 0.14 cycle difference between duplicated reactions.
Similarly, the standard deviation increases 0.07 units per 0.1 cycle difference between duplicated reactions. Hence, if you want to flag bad duplicates that differ by more than 0.2 standard deviations, you need to use a 0.28 cycle difference.
For triplicates, a standard deviation threshold of 0.1 means that the highest and lowest Cq value can only differ by maximum 0.1 Cq values from the middle point.