designed to be reasonably large . Assume that the positive and negative controls in a plate have sample mean , sample variances , and sample sizes . Usually, the assumption that the controls have equal variance in a plate holds. In such a case, The SSMD for assessing quality in that plate is estimated as where . When the assumption of equal variance does not hold, the SSMD for assessing quality in that plate is estimated as If there are clearly outliers in the controls, the SSMD can be estimated as where are the medians and median absolute deviations in the positive and negative controls, respectively. The Z-factor based QC criterion is popularly used in HTS assays. However, it has been demonstrated that this QC criterion is most suitable for an assay with very or extremely strong positive controls. In an RNAi HTS assay, a strong or moderate positive control is usually more instructive than a very or extremely strong positive control because the effectiveness of this control is more similar to the hits of interest. In addition, the positive controls in the two HTS experiments theoretically have different sizes of effects. Consequently, the QC thresholds for the moderate control should be different from those for the strong control in these two experiments. Furthermore, it is common that two or more positive controls are adopted in a single experiment. Applying the same Z-factor-based QC criteria to both controls leads to inconsistent results as illustrated in the literatures. The SSMD-based QC criteria listed in the following table take into account the effect size of a positive control in an HTS assay where the positive control (such as an inhibition control) theoretically has values less than the negative reference. In application, if the effect size of a positive control is known biologically, adopt the corresponding criterion based on this table. Otherwise, the following strategy should help to determine which QC criterion should be applied: (i) in many small molecule HTS assay with one positive control, usually criterion D (and occasionally criterion C) should be adopted because this control usually has very or extremely strong effects; (ii) for RNAi HTS assays in which cell viability is the measured response, criterion D should be adopted for the controls without cells (namely, the wells with no cells added) or background controls; (iii) in a viral assay in which the amount of viruses in host cells