A comparison of methods for differential expression analysis of RNA-seq data

BMC Bioinformatics

Table 1 The number of shared differentially expressed genes found by the different methods for the Bottomly data set

	ShrinkSeq	DESeq	edgeR	NBPSeq	TSPM	voom	vst	baySeq	EBSeq	SAMseq
ShrinkSeq	3259	583	1125	985	1075	971	1049	192	803	1821
DESeq	583	598	598	567	588	589	587	191	523	592
edgeR	1125	598	1160	877	886	942	1013	194	753	1099
NBPSeq	985	567	877	1082	695	753	797	194	612	924
TSPM	1075	588	886	695	1161	891	907	191	794	1014
voom	971	589	942	753	891	1009	971	194	752	991
vst	1049	587	1013	797	907	971	1095	194	752	1061
baySeq	192	191	194	194	191	194	194	195	175	194
EBSeq	803	523	753	612	794	752	752	175	819	801
SAMseq	1821	592	1099	924	1014	991	1061	194	801	1860

The table contains the number of differentially expressed genes that are shared between each pair of methods, for the Bottomly data set (compare to Figure 5). The numbers on the diagonal, indicating the number of differentially expressed genes found by the respective methods, are highlighted in bold.

ISSN: 1471-2105