Agreeing to disagree, some ironies, disappointing scientific practice and a call for better: reply to The poor performance of TMM on microRNA-Seq

Agreeing to disagree, some ironies, disappointing scientific practice and a call for better: reply to The poor performance of TMM on microRNA-Seq
Mark D. Robinson
(Submitted on 27 May 2013)

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

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