Venn diagrams of differentially expressed (DE) transcripts.

<p>Two RNA-Seq datasets with one replicate (A) and two replicates (B) in each class. Five different methods, i.e., LPEseq (brown), edgeR (sky blue), DESeq (green), DESeq2 (violet) and NBPSeq (red) were used. A density plot of the mean difference between classes of uniquely found DE transcripts in each method was indicated. X- and Y-axis represent group mean difference and density. The number in parentheses indicates the total number of DE transcripts found. The criterion used to call DE was Benjamini-Hochberg corrected p-value less than 0.05 for all methods. The enriched terms gene set analysis was performed by DAVID web-tool.