Figure 3
From: MBASED: allele-specific expression detection in cancer tissues and cell lines
Performance of MBASED on simulated data in two-sample analysis. Simulations were performed similar to the one-sample case, as described in Materials and methods. MBASED was run on the simulated data and genes with Benjamini-Hochberg adjusted P-values ≤0.05 (false discovery rate (FDR) control of 5%) were declared ASE. The average (across 100 simulations) true positive rate (TPR) and FDR within each strata and for each level of ASE signal (MAF used for ASE true positive genes) are shown. The overall TPR and FDR levels are obtained by giving each stratum weight proportional to the fraction of genes in that stratum (that is, these values are heavily weighted towards genes with few SNVs and low coverage, common in our data), and the average values are given in panel titles, along with their estimated standard errors (SE). MBASED performs well at higher coverage levels and higher ASE extent, but its power is limited for the low-coverage, low-signal scenarios.