Exclude PCR replicates that do not meet quality control criteria
qbase+ flags bad replicates based on a user defined maximum allowed difference in Cq values (defined in the Experiment quality control settings), but does not automatically exclude outliers.
This means that the experimenter needs to decide what to do with the failing replicates (in Replicates window).
In addition to the (default) arithmetic mean on replicated Cq value measurements, qbase+ also supports the calculation of median Cq values (option in the Calculation parameters window).
The median Cq value represents a more robust measure than the arithmetic mean when confronted with outliers and having at least 3 PCR replicates. Median results (without outlier removal) are a good alternative to arithmetic averages with outlier removal.