is the interest, criterion C is usually used, and criterion D is occasionally used for the positive control consisting of siRNA from the virus. Similar SSMD-based QC criteria can be constructed for an HTS assay where the positive control (such as an activation control) theoretically has values greater than the negative reference. More details about how to apply SSMD-based QC criteria in HTS experiments can be found in a book. Hit selection In an HTS assay, one primary goal is to select compounds with a desired size of inhibition or activation effect. The size of the compound effect is represented by the magnitude of difference between a test compound and a negative reference group with no specific inhibition/activation effects. A compound with a desired size of effects in an HTS screen is called a hit. The process of selecting hits is called hit selection. There are two main strategies of selecting hits with large effects. One is to use certain metric(s) to rank and/or classify the compounds by their effects and then to select the largest number of potent compounds that is practical for validation assays. The other strategy is to test whether a compound has effects strong enough to reach a pre-set level. In this strategy, false-negative rates (FNRs) and/or false-positive rates (FPRs) must be controlled. SSMD can not only rank the size of effects but also classify effects as shown in the following table based on the population value () of SSMD. The estimation of SSMD for screens without replicates differs from that for screens with replicates. In a primary screen without replicates, assuming the measured value (usually on the log scale) in a well for a tested compound is and the negative reference in that plate has sample size , sample mean , median , standard deviation and median absolute deviation , the SSMD for this compound is estimated as where . When there are outliers in an assay which is usually common in HTS experiments, a robust version of SSMD can be obtained using In a confirmatory or primary screen with replicates, for the i-th test compound with replicates, we calculate the paired difference between the measured value (usually on the log scale) of the compound and the median value of a negative control in a plate, then obtain the mean and variance of the paired difference across replicates. The SSMD for this compound is estimated