Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Seq

This work quantitatively explores comparisons between contemporary analysis tools and experimental design choices for the detection of differential expression using RNA-Seq. The authors found that the DESeq algorithm performs more conservatively than edgeR and NBPSeq. With regard to testing of various experimental designs, this work strongly suggests that greater power is gained through the use of biological replicates relative to library (technical) replicates and sequencing depth. Strikingly, sequencing depth could be reduced as low as 15% without substantial impacts on false positive or true positive rates.

Robles JA, Qureshi SE, Stephen SJ, Wilson SR, Burden CJ, Taylor JM. (2012) Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing. BMC Genomics 13(1), 484. [article]