The q-value (or False Discovery Rate [16]) explicitly incorporates the vastness of the genome in the calculation. The q-value of a transcription factor binding site tells us the proportion of sites of that strength or better that we expect to be false positives. Under ideal circumstances, the researcher who chooses a q-value threshold of 0.001 expects only one in 1,000 of the reported sites to be a false positive regardless of the genome size. (However, because we do not pretend to have statistically modeled all the relevant biology, the false discovery rate will generally be higher than the specified threshold.)