Table 4.

Significant genes detected from the dataset in Marioni et al (2008).

Significant Genes in Intersecting Sets
Method	EBA (Affymetrix)	(LRT)	EBA (RNA-Seq)	edgeR	DESeq
EBA (Affymetrix)	3641	3096	672	3127	3037	251	3183	960
(LRT)		8641	790	8461	5400	308	8641	1116
EBA (RNA-Seq)			790	790	789	275	790	700
edgeR				8697	5516	308	8697	1351
DESeq					7083	301	5644	1305
						315	308	315
							11915	3324
								3331

For each row and column, the number gives the significant gene calls by both methods. The cut-off to determine significance was set at α = 0.05/32000. The acronym LRT denotes the likelihood ratio test based on the Poisson distribution, as described in the Methods. The acronym EBA denotes the empirical Bayes analysis performed on both the Affymetrix and RNA-Seq data.