Please use this identifier to cite or link to this item:
http://hdl.handle.net/1942/31792
Full metadata record
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Hawinkel, Stijn | - |
dc.contributor.author | Rayner, J. C. W. | - |
dc.contributor.author | BIJNENS, Luc | - |
dc.contributor.author | THAS, Olivier | - |
dc.date.accessioned | 2020-08-24T08:07:13Z | - |
dc.date.available | 2020-08-24T08:07:13Z | - |
dc.date.issued | 2020 | - |
dc.date.submitted | 2020-08-13T10:20:15Z | - |
dc.identifier.citation | PLOS ONE, 15 (4) (Art N° e0224909) | - |
dc.identifier.uri | http://hdl.handle.net/1942/31792 | - |
dc.description.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. | - |
dc.description.sponsorship | Stijn Hawinkel was funded by Janssen Pharmaceutical Companies of John-son and Johnson. Luc Bijnens is currently employed by Janssen Pharmaceu-tical 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. | - |
dc.language.iso | en | - |
dc.publisher | PUBLIC LIBRARY SCIENCE | - |
dc.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. | - |
dc.subject.other | Goodness-Of-Fit | - |
dc.subject.other | Rna-Seq Data | - |
dc.subject.other | Models | - |
dc.title | Sequence count data are poorly fit by the negative binomial distribution | - |
dc.type | Journal Contribution | - |
local.bibliographicCitation.authors | Kumar, Shailesh | - |
dc.identifier.issue | 4 | - |
dc.identifier.volume | 15 | - |
local.format.pages | 16 | - |
local.bibliographicCitation.jcat | A1 | - |
dc.description.notes | Hawinkel, S (corresponding author), Univ Ghent, Dept Data Anal & Math Modelling, Ghent, Belgium. | - |
dc.description.notes | stijn.hawinkel@ugent.be | - |
dc.description.other | Hawinkel, S (corresponding author), Univ Ghent, Dept Data Anal & Math Modelling, Ghent, Belgium. stijn.hawinkel@ugent.be | - |
local.publisher.place | 1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA | - |
local.type.refereed | Refereed | - |
local.type.specified | Article | - |
local.bibliographicCitation.artnr | e0224909 | - |
dc.identifier.doi | 10.1371/journal.pone.0224909 | - |
dc.identifier.pmid | 32352970 | - |
dc.identifier.isi | WOS:000536673200005 | - |
dc.contributor.orcid | Bijnens, Luc/0000-0002-4126-3152; Rayner, John/0000-0003-4987-0026 | - |
local.provider.type | wosris | - |
local.uhasselt.uhpub | yes | - |
local.description.affiliation | [Hawinkel, Stijn; Thas, Olivier] Univ Ghent, Dept Data Anal & Math Modelling, Ghent, Belgium. | - |
local.description.affiliation | [Rayner, J. C. W.] Univ Newcastle, Ctr Comp Assisted Res Math & Its Applicat, Sch Math & Phys Sci, Newcastle, NSW, Australia. | - |
local.description.affiliation | [Bijnens, Luc] Janssen Pharmaceut Co Johnson & Johnson, Quantitat Sci, Ghent, Belgium. | - |
local.description.affiliation | [Bijnens, Luc; Thas, Olivier] Hasselt Univ, I BioStat, Hasselt, Belgium. | - |
local.description.affiliation | [Rayner, J. C. W.; Thas, Olivier] Univ Wollongong, Natl Inst Appl Stat Res Australia NIASRA, Wollongong, NSW, Australia. | - |
item.validation | ecoom 2021 | - |
item.contributor | Hawinkel, Stijn | - |
item.contributor | Rayner, J. C. W. | - |
item.contributor | BIJNENS, Luc | - |
item.contributor | THAS, Olivier | - |
item.accessRights | Open Access | - |
item.fullcitation | Hawinkel, Stijn; Rayner, J. C. W.; BIJNENS, Luc & THAS, Olivier (2020) Sequence count data are poorly fit by the negative binomial distribution. In: PLOS ONE, 15 (4) (Art N° e0224909). | - |
item.fulltext | With Fulltext | - |
crisitem.journal.issn | 1932-6203 | - |
crisitem.journal.eissn | 1932-6203 | - |
Appears in Collections: | Research publications |
Files in This Item:
File | Description | Size | Format | |
---|---|---|---|---|
Hawinkel_Stijn_2020.pdf | Published version | 1.06 MB | Adobe PDF | View/Open |
WEB OF SCIENCETM
Citations
24
checked on Apr 30, 2024
Page view(s)
64
checked on Jul 15, 2022
Download(s)
16
checked on Jul 15, 2022
Google ScholarTM
Check
Altmetric
Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.