ArticlePloS one2020
Sequence count data are poorly fit by the negative binomial distribution.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Functional Redundancy Enables Stable Treatment Performance Across Taxonomically Diverse Dairy Wastewater Microbiomes.Environmental microbiology reports · 2026Pooled it
- Evaluating statistical models for overdispersed multiomics data: a multiplex immunofluorescence case study.American journal of epidemiology · 2026Article
- Article
- Reproducible Tools and Enhanced Computational Workflows for Batch Effect Evaluation of High-Throughput Data Using BatchQC.bioRxiv : the preprint server for biology · 2026Article
- NBSR: a Negative Binomial Softmax Regression model for microRNA-seq data analysis.Biostatistics (Oxford, England) · 2026Article
- Poisson Beta Regression for Count Data With an Application to Hospital Length of Stay Data.Statistics in medicine · 2025Article
- Detecting differential transcript usage in complex diseases with SPIT.Cell reports methods · 2024Article
- Detecting differential transcript usage in complex diseases with SPIT.bioRxiv : the preprint server for biology · 2023Article
- Benchmarking differential abundance analysis methods for correlated microbiome sequencing data.Briefings in bioinformatics · 2023Article
- Simple and flexible sign and rank-based methods for testing for differential abundance in microbiome studies.PloS one · 2023Article
- llperm: a permutation of regressor residuals test for microbiome data.BMC bioinformatics · 2022Article
- Investigating differential abundance methods in microbiome data: A benchmark study.PLoS computational biology · 2022Review
- Differential expression of single-cell RNA-seq data using Tweedie models.Statistics in medicine · 2022Article
- Exaggerated false positives by popular differential expression methods when analyzing human population samples.Genome biology · 2022Article
- Randomized quantile residuals for diagnosing zero-inflated generalized linear mixed models with applications to microbiome count data.BMC bioinformatics · 2021Article
- Multivariable association discovery in population-scale meta-omics studies.PLoS computational biology · 2021Article
- Chi-square test under indeterminacy: an application using pulse count data.BMC medical research methodology · 2021Article
- Neutrosophic statistical test for counts in climatology.Scientific reports · 2021Article
- Data Analysis Strategies for Microbiome Studies in Human Populations-a Systematic Review of Current Practice.mSystems · 2021Article
- Exploring the Microbiome Analysis and Visualization Landscape.Frontiers in bioinformatics · 2021Review
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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 nonparametric tests should be preferred over parametric methods.
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