A new pooling strategy for high-throughput screening: the Shifted Transversal Design

BMC Bioinformatics

Table 1 Choosing the optimal value for the number of pools per layer, q

This table shows the gains obtained with various q values, when the total number of variables to be tested is n = 10000 and the number of expected positives is t = 5, in a noiseless experiment (E = 0). Γ is the compression power (i.e. logarithm of n in base q, see Preliminaries in Results(1) section), k is the number of layers, v is the number of pools (i.e. k·q), and the gain is defined as n/v. By construction, STD requires k ≤ q+1; and to guarantee the identification of t positives while correcting E errors, section 3.3 showed that we must choose k = t·Γ+2·E+1; in this example, k = 5Γ+1. Often, the smallest useable q (i.e., satisfying k ≤ q+1), q_min, yields the highest gain, but this is not always the case. In this example, q_min = 17, but q = 23 (smallest q such that Γ = 2) yields the highest gain: 39.5.

ISSN: 1471-2105