The Debate Rages On!

A systematic comparison of RNA-Seq and High-Density Exon Array for detecting differential gene expression between closely related species (a panel of human/chimpanzee/rhesus cerebellum RNA samples).

  • Results indicate that RNA-Seq has significantly improved gene coverage and increased sensitivity for differentially expressed genes compared with the high-density array.
  • Low expression level DEGs detected by array/qPCR were missed by RNA-Seq.
  • RNA-Seq analysis showed an increase in both the false-negative rate and the false-positive rate for lowly expressed genes.

Liu S, Lin L, Jiang P, Wang D, Xing Y. (2010) A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. Nucleic Acids Res [Epub ahead of print].  [abstract]