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

TL;DR

This paper critiques a previous study on microRNA-Seq normalization, clarifies misunderstandings with supporting code and evidence, and advocates for improved scientific practices in the field.

Contribution

It provides a detailed rebuttal to misinterpretations of a normalization method, emphasizing the importance of reproducibility and accurate communication in scientific research.

Findings

Corrected misuse of the normalization method

Highlighted the importance of reproducible code

Called for better scientific practices

Abstract

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.