Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols

Table 4 Concordance for gene sets found in gene set analysis using the camera function

^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

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