The poor performance of TMM on microRNA-Seq.

Background. This letter is a response to a Divergent Views article entitled “The poor 8 performance of TMM on microRNA-Seq” (Garmire and Subramaniam 2013), which was a 9 response to our Divergent Views article entitled “miRNA-seq normalization comparisons need 10 improvement” (Zhou et al. 2013). Using reproducible code examples, we showed that they 11 incorrectly used our normalization method and highlighted additional concerns with their study. 12 Here, I wish to debunk several untrue or misleading statements made by the authors (hereafter 13 referred to as GS) in their response. Unlike GS’s, my claims are supported by R code, citations 14 and email correspondences. I finish by making a call for better practice. 15