Additional file 2.

Figure S4. Venn-diagram showing the TP and FP calls made by DESeq (left, blue circle) and edgeR (right, red circle) and how they overlap between each other and the total pool of transcripts designated as truly DE (top, green circle). A: the Venn-diagram for the case in which the number of biological replicates is n = 12 and depth is 100%. This combination of n and depth is somewhat unrealistic as the cost of 24 lanes of sequencing would be almost prohibitive; however, it shows a ‘best case scenario’ situation in which 2870 of the total 5689 truly DE transcripts were detected by the union of DESeq and edgeR. Of these 2870 TP detections, most of them (2360) were detected by both algorithms – hence either algorithm would have sufficed. B: the Venn-diagram for n = 4 and depth is 25%. This more realistic experimental design choice of n and depth shows the value of using both algorithms; only 913 out of the total 5697 truly DE transcripts were detected by both algorithms, only two thirds of them (591) were detected by both algorithms. These contrasting scenarios show that the use of both algorithms aids to further constrain the list of viable DE candidates in a fast and cheap manner.

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Robles et al. BMC Genomics 2012 13:484   doi:10.1186/1471-2164-13-484