Comparing six DE methods on a 4 vs 4 comparison. One hundred random comparisons of four B6 and four D2 mouse striatum samples for six DE methods. Average TP and FP are calculated for the full range of p-value cut-offs. The TPR and FPR are plotted against each other in a) to form ROC curves and displayed in the region for FPR less than 0.01 as this is most relevant for calling DE. For any given FPR a method with a larger TPR is deemed to have ranked the genes better. In b) the number of TP (in bold) and FP are plotted for a range of p-value cut-offs. The x-axis is in log-scale. The grey dashed vertical line corresponds to a Bonferroni adjusted cut-off of 0.05.
Patrick et al. BMC Genomics 2013 14(Suppl 1):S9 doi:10.1186/1471-2164-14-S1-S9