Figure 3.

Log likelihood and FDR plot. Minus log likelihood versus the FDR threshold (l) for different genes in one of the simulated data (proportion of cancer-type specific and metastatic related differentially expressed genes: p = q = 0.1; degree of effect: |Δ| = 1). FDR is the proportion of false positives among genes declared to be differentially expressed for each dataset. The dotted line represents genes that are consistently differentially expressed, solid line represents genes that are differentialy expressed only in specific dataset, and dashed line represents non-differentially expressed genes. The three lines show the mean, and the vertical bars show the standard deviation of the Q values for the three types of genes at the given FDR. For clarity, only the upper bars are shown.