Evaluate RNAseq DEG software

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

Genome Biology 2013, 14:R95  doi:10.1186/gb-2013-14-9-r95

 

Differential expression analysis using qRT-PCR validated gene set. (a) ROC analysis was performed using a qRT-PCR log₂ expression change threshold of 0.5. The results show a slight advantage for DESeq and edgeR in detection accuracy. (b) At increasing log₂ expression ratios (incremented by 0.1), representing a more stringent cutoff for differential expression, the performances of the Cuffdiff and limma methods gradually reduce whereas PoissonSeq performance increases. AUC, area under the curve.

Rapaport et al. Genome Biology 2013 14:R95   doi:10.1186/gb-2013-14-9-r95