Additional file 2: of Evaluation of methods for differential expression analysis on multi-group RNA-seq count data

Results for simulation data with replicates (mainly Nrep = 6 and 9). Average AUC values (%) of 100 trials are shown for a total of 12 pipelines for three-group simulation data, where each group has six (Nrep = 6; Sheet 1) and nine (Nrep = 9; Sheet 2) BRs. Sheet 3: Average partial AUC values (%) of 20 trials with (1 - specificity) < 0.1. Sheet 4: Average computation times (in seconds) of 20 trials. The times were measured on a Windows system (Windows 7 Professional, Intel(R) Core(TM) i5-2540 M CPU, 2.60 GHz, and 8 GB memory). Sheet 5: Average AUC values (%) of 20 trials where the fold-changes for DEGs were randomly sampled from “1.2 + a gamma distribution with shape = 2.0 and scale = 0.5”. Other legends are the same as in Table 1. (XLSX 24 kb)