Table 4.

Concordance for gene sets found in gene set analysis using the camera function

PE vs SE	Exp 1a	Exp 2a	Exp 3a	Exp 4a
Top 50 gene sets	100	98	96	98
Top 100	98	98	98	97
Top 200	99	99	97	99
Top 400	99	PE total 243	98	99
PE vs NS		Exp 2b	Exp 3b	Exp 4b
Top 50 gene sets		98	96	98
Top 100		97	94	93
Top 200		99	96	99
Top 400		PE total 243	96	96

^aPercentage concordance in the top gene sets (by FDR) found using the camera function of limma when using the SE and PE datasets for each of the experiments

^bPercentage concordance in the top top gene sets (by FDR) found using the camera function of limma when using the PE strand specific and non-strand specific datasets for experiments 2–4