The High Contrast versus Self-Self method (HCSSM). The figure illustrates how the false discovery rate is determined in HCSSM. For a chosen T cut-off, the genes with T-scores larger than the cut-off are declared significant. The false discovery rate is then determined by dividing the number of genes deemed significant in the self-self experiment by the number of genes deemed significant in the high contrast experiment. For example, if for a T-cut-off six genes are declared significant from the self-self experiment and 127 genes are declared significant from the high contrast experiment the false discovery rate will be 6/127 ~0.05. If a specific false discovery rate is wanted (often 0.05 or 0.01), the T cut-off can be adjusted to obtain it.