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Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
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Bayesian estimation of differential transcript usage from RNA-seq data.

Panagiotis Papastamoulis1, Magnus Rattray1

  • 1.

Statistical Applications in Genetics and Molecular Biology
|November 2, 2017
PubMed
Summary
This summary is machine-generated.

This study introduces Bayesian approaches for differential transcript usage (DTU) analysis, extending cjBitSeq and proposing BayesDRIMSeq. These methods offer improved False Discovery Rate calibration compared to existing models.

Keywords:
Laplace approximationMCMCalternative splicingfalse discovery ratewithin gene transcript expression

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Differential transcript usage (DTU) analyzes changes in relative transcript expression within genes, distinct from overall expression levels.
  • Next-generation sequencing (NGS) technologies enable the identification of differentially expressed transcripts.

Purpose of the Study:

  • To extend the Bayesian model cjBitSeq for differential transcript usage (DTU) analysis.
  • To propose BayesDRIMSeq, a novel Bayesian version of the frequentist DRIMSeq model for DTU inference.
  • To evaluate the performance of these Bayesian methods against existing models.

Main Methods:

  • cjBitSeq: A read-based Bayesian model using MCMC sampling for transcript-level inference.
  • BayesDRIMSeq: A count-based Bayesian model estimating Bayes Factors via Laplace approximation.
  • Benchmarking using simulation studies and a real RNA-seq dataset.

Main Results:

  • Bayesian methods (cjBitSeq and BayesDRIMSeq) demonstrate comparable precision and recall to the frequentist DRIMSeq.
  • The proposed Bayesian models provide superior calibration of the False Discovery Rate (FDR).

Conclusions:

  • Bayesian inference offers a robust alternative for differential transcript usage analysis.
  • The developed Bayesian methods enhance the reliability of DTU findings through improved FDR control.