ArticleBioinformatics (Oxford, England)2019
PairedFB: a full hierarchical Bayesian model for paired RNA-seq data with heterogeneous treatment effects.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- lmerSeq: an R package for analyzing transformed RNA-Seq data with linear mixed effects models.BMC bioinformatics · 2022Article
- A comparison of methods for multiple degree of freedom testing in repeated measures RNA-sequencing experiments.BMC medical research methodology · 2022Article
- MCMSeq: Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments.BMC bioinformatics · 2020Article
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5 authors.
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Abstract
motivationSeveral methods have been proposed for the paired RNA-seq analysis. However, many of them do not consider the heterogeneity in treatment effect among pairs that can naturally arise in real data. In addition, it has been reported in literature that the false discovery rate (FDR) control of some popular methods has been problematic. In this paper, we present a full hierarchical Bayesian model for the paired RNA-seq count data that accounts for variation of treatment effects among pairs and controls the FDR through the posterior expected FDR.
resultsOur simulation studies show that most competing methods can have highly inflated FDR for small to moderate sample sizes while PairedFB is able to control FDR close to the nominal levels. Furthermore, PairedFB has overall better performance in ranking true differentially expressed genes (DEGs) on the top than others, especially when the sample size gets bigger or when the heterogeneity level of treatment effects is high. In addition, PairedFB can be applied to identify the biologically significant DEGs with controlled FDR. The real data analysis also indicates PairedFB tends to find more biologically relevant genes even when the sample size is small. PairedFB is also shown to be robust with respect to the model misspecification in terms of its relative performance compared to others. AVAILABILITY AND IMPLEMENTATION: Software to implement this method (PairedFB) can be downloaded at: https://sites.google.com/a/udel.edu/qiujing/publication. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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