9/9/2023 0 Comments Negative binomialBoxplots of estimated feature-specific dispersion parameters of the negative binomial distribution per dataset. As evident from Fig 1, the overdispersion varies between features and depends on the biological nature of the samples, being notably large for microbiome data of human origin.įig 1. This overdispersion is also strongly related to the frequency of zeroes in the count data. The NB distribution can be seen as a extension of the Poisson distribution that allows for overdispersion due to the biological variability. It is often assumed that the sequence counts from a single feature (either a taxon or a gene) follow the negative binomial (NB) distribution. Apart from the biological variability between samples, the multiple manipulations, going from nucleic acid extraction, reverse transcription and PCR amplification to actual sequencing, introduce additional variability into the feature count tables. As both research areas employ the same technologies, their data properties and analysis techniques are similar. The resulting collection of sequences is then considered as a proxy for the transcriptomic state of a tissue or cell (in RNA-Seq) or for the species composition (for the microbiome). In research areas such as RNA-sequencing (RNA-Seq) and microbiomics, sequencing technologies are applied to measure the composition of mixtures of nucleic acids. This does not alter our adherence to PLOS ONE policies on sharing data and materials. Luc Bijnens is currently employed by Janssen Pharmaceutical Companies of Johnson and Johnson. The funders supervised the work and provided suggestions, but had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: Stijn Hawinkel was funded by Janssen Pharmaceutical Companies of Johnson and Johnson. Luc Bijnens is currently employed by Janssen Pharmaceu- tical Companies of Johnson and Johnson. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: All relevant data are within the manuscript and its Supporting Information files.įunding: Stijn Hawinkel was funded by Janssen Pharmaceutical Companies of John- son and Johnson. Received: OctoAccepted: ApPublished: April 30, 2020Ĭopyright: © 2020 Hawinkel et al. National Institute of Plant Genome Research (NIPGR), INDIA Citation: Hawinkel S, Rayner JCW, Bijnens L, Thas O (2020) Sequence count data are poorly fit by the negative binomial distribution.
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