RoPE: A robust profile likelihood method for differential gene expression analysis.
Genet Epidemiol
; 47(5): 379-393, 2023 07.
Article
em En
| MEDLINE
| ID: mdl-37042632
ABSTRACT
Variation in RNA-Seq data creates modeling challenges for differential gene expression (DE) analysis. Statistical approaches address conventional small sample sizes and implement empirical Bayes or non-parametric tests, but frequently produce different conclusions. Increasing sample sizes enable proposal of alternative DE paradigms. Here we develop RoPE, which uses a data-driven adjustment for variation and a robust profile likelihood ratio DE test. Simulation studies show RoPE can have improved performance over existing tools as sample size increases and has the most reliable control of error rates. Application of RoPE demonstrates that an active Pseudomonas aeruginosa infection downregulates the SLC9A3 Cystic Fibrosis modifier gene.
Palavras-chave
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Perfilação da Expressão Gênica
/
Modelos Genéticos
Tipo de estudo:
Prognostic_studies
Limite:
Humans
Idioma:
En
Ano de publicação:
2023
Tipo de documento:
Article