Stability of methods for differential expression analysis of RNA-seq data

BMC Genomics

Table 1 Summary of stability levels based on AUCOR

	edgeR	edgeR_robust	DESeq_glm	DESeq2	EBSeq	Voom
Low replicate number	+	+	+	++	-	–
(2 to 4)
High replicate number	+	-	++	+	+	++
(> 4)
Low fold change	+	+	–	+	+	–
(< 3)
High fold change	+	+	+	+	-	+
(> 3)
Low dispersion	+	+	-	+	+	–
(< 1)
High dispersion	+	+	+	+	+	+
(> 1)
No outliers	+	+	+	+	+	+
Outliers	-	+	–	++	++	–
Low expressed features	+	+	+	-	-	+
High expressed features	+	+	-	+	-	+

ISSN: 1471-2164