Fig. 2
From: Evaluation of methods for differential expression analysis on multi-group RNA-seq count data
Reproducibility between ranked gene lists. Numbers of common genes between top-ranked genes for individual pipelines are shown: (a) results for 100 top-ranked gene lists and (b) results for 1000 top-ranked gene lists. Bars in black (rep1-6 vs. rep1-2), gray (rep1-6 vs. rep3-4), and blue (rep1-6 vs. rep5-6) in Fig. 2a indicate the numbers of common genes between the two sets of 100 top-ranked genes obtained from the individual pipelines. For example, the gray bar (rep1-6 vs. rep3-4) for DDD-D in Fig. 2a indicates that there were 46 common genes when the 100 top-ranked genes from the dataset rep1-6 are compared with the 100 top-ranked genes from the dataset rep3-4. Analogously, bars in red (rep1-2 vs. rep3-4 vs. rep5-6) in Fig. 2b indicate the numbers of common genes between the three sets of 1000 top-ranked genes for the three datasets (rep1-2, rep3-4, and rep5-6). For example, the red bar for EEE-E in Fig. 2b indicates that there were 397 common genes (39.7 % of overlapping genes) when the three sets of gene lists (each of which contains 1000 top-ranked genes) obtained from the pipeline EEE-E for the three datasets were compared. The full R code for this analysis is given in Additional file 5