Detecting differentially expressed genes with RNA-seq data using backward selection to account for the effects of relevant covariates

DOI10.1007/S13253-015-0226-1MaRDI QIDQ906078zbMATH OpenOpenAlexWikidataFDO

Authors Dan Nettleton, Haibo Liu, Christopher K. Tuggle, Yet Tien Nguyen

Publication date 29 January 2016

Published in Journal of Agricultural, Biological and Environmental Statistics (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://doi.org/10.1007/s13253-015-0226-1

zbMATH Keywords

false discovery rategeneralized linear modelquasi-likelihoodresidual feed intake

Mathematics Subject Classification ID

Applications of statistics to environmental and related topics (62P12) Protein sequences, DNA sequences (92D20)

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Cites work

• scientific article; zbMATH DE number 3126936 (Why is no real title available?)
• scientific article; zbMATH DE number 1906319 (Why is no real title available?)
• A Direct Approach to False Discovery Rates
• Adaptive and Dynamic Adaptive Procedures for False Discovery Rate Control and Estimation
• Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates
• Small-sample estimation of negative binomial dispersion, with applications to SAGE data
• The NBP negative binomial model for assessing differential gene expression from RNA-Seq

Cited in

(5)

• Hierarchical modeling and differential expression analysis for RNA-seq experiments with inbred and hybrid genotypes
• A Markov random field-based approach for joint estimation of differentially expressed genes in mouse transcriptome data
• What if we ignore the random effects when analyzing RNA-seq data in a multifactor experiment
• Detection of differentially expressed genes in discrete single‐cell RNA sequencing data using a hurdle model with correlated random effects
• Homology cluster differential expression analysis for interspecies mRNA-seq experiments

Describes a project that uses

Uses Software

• R
• Bioconductor
• BaySeq
• DEseq
• RUVseq
• limma
• QuasiSeq
• ShrinkBayes
• Voom
• svaseq

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