期刊
GENETIC EPIDEMIOLOGY
卷 47, 期 5, 页码 379-393出版社
WILEY
DOI: 10.1002/gepi.22526
关键词
cystic fibrosis lung infection; differential expression analysis; overdispersion; profile likelihood inference; RNA-Seq; robust adjustment
Variation in RNA-Seq data presents modeling challenges for DE analysis. Statistical methods address small sample sizes but often produce different conclusions. RoPE, a new approach, adjusts for variation and uses a robust DE test, showing improved performance and reliable error rate control.
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.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据