Fig. 5

Application of Clipper, DESeq2, and edgeR to identifying DEGs from the classical and non-classical human monocyte dataset. a A Venn diagram showing the overlaps of the identified DEGs (at the FDR threshold q=5%) by the three DE methods. b Numbers of GO terms enriched (with enrichment q-values <0.01) in the DEGs found by Clipper, DESeq2, and edgeR (column 3), or in the DEGs specifically identified by Clipper or DESeq2/edgeR in the pairwise comparison between Clipper and DESeq2 (column 1) or between Clipper and edgeR (column 2). More GO terms are enriched in the DEGs identified by Clipper than in those identified by edgeR or DESeq2. c Enrichment q-values of four GO terms that are found enriched (with enrichment q-values <0.01) in all three sets of identified DEGs, one set per method. All the four terms are most enriched in the DEGs identified by Clipper. d A scatterplot of the claimed FDR of Clipper against that of edgeR for all the DEGs identified by Clipper, edgeR or DESeq2. The 46 DEGs identified by Clipper only at 5% FDR are highlighted in red