No counts, no variance: allowing for loss of degrees of freedom when assessing biological variability from RNA-seq data

DOI10.1515/sagmb-2017-0010zbMath1371.92054OpenAlexW2621124619WikidataQ36397098 ScholiaQ36397098MaRDI QIDQ2406178

Gordon K. Smyth, Aaron T. L. Lun

Publication date: 27 September 2017

Published in: Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1515/sagmb-2017-0010

zbMATH Keywords

differential expressionquasi-likelihoodgeneralized linear modelsRNA sequencing

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40)

Uses Software

• Bioconductor
• edgeR
• DEseq
• limma
• QuasiSeq
• Voom
• featureCounts
• csaw
• diffHic

Cites Work

• Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates
• Bioconductor
• Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression
• Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
• Fitting Tweedie's Compound Poisson Model to Insurance Claims Data: Dispersion Modelling
• Unnamed Item

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