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http://hdl.handle.net/1942/31792
Title: | Sequence count data are poorly fit by the negative binomial distribution | Authors: | Hawinkel, Stijn Rayner, J. C. W. BIJNENS, Luc THAS, Olivier |
Issue Date: | 2020 | Publisher: | PUBLIC LIBRARY SCIENCE | Source: | PLOS ONE, 15 (4) (Art N° e0224909) | Abstract: | Sequence count data are commonly modelled using the negative binomial (NB) distribution. Several empirical studies, however, have demonstrated that methods based on the NB-assumption do not always succeed in controlling the false discovery rate (FDR) at its nominal level. In this paper, we propose a dedicated statistical goodness of fit test for the NB distribution in regression models and demonstrate that the NB-assumption is violated in many publicly available RNA-Seq and 16S rRNA microbiome datasets. The zero-inflated NB distribution was not found to give a substantially better fit. We also show that the NB-based tests perform worse on the features for which the NB-assumption was violated than on the features for which no significant deviation was detected. This gives an explanation for the poor behaviour of NB-based tests in many published evaluation studies. We conclude that non-parametric tests should be preferred over parametric methods. | Notes: | Hawinkel, S (corresponding author), Univ Ghent, Dept Data Anal & Math Modelling, Ghent, Belgium. stijn.hawinkel@ugent.be |
Other: | Hawinkel, S (corresponding author), Univ Ghent, Dept Data Anal & Math Modelling, Ghent, Belgium. stijn.hawinkel@ugent.be | Keywords: | Goodness-Of-Fit;Rna-Seq Data;Models | Document URI: | http://hdl.handle.net/1942/31792 | ISSN: | 1932-6203 | e-ISSN: | 1932-6203 | DOI: | 10.1371/journal.pone.0224909 | ISI #: | WOS:000536673200005 | Rights: | © 2020 Hawinkel et al. 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. | Category: | A1 | Type: | Journal Contribution | Validations: | ecoom 2021 |
Appears in Collections: | Research publications |
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Hawinkel_Stijn_2020.pdf | Published version | 1.06 MB | Adobe PDF | View/Open |
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