Controlling the false-discovery rate by procedures adapted to the length bias of RNA-seq

DOI10.1016/J.JKSS.2017.08.001MaRDI QIDQ684055zbMATH OpenOpenAlexFDO

Authors Tae Young Yang, Seongmun Jeong

Publication date 9 February 2018

Published in Journal of the Korean Statistical Society (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jkss.2017.08.001

zbMATH Keywords

length biasRNA-Seqcommon weightindividual weightseparate procedureweighted procedure

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Protein sequences, DNA sequences (92D20)

Recommendations

• Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates
• Modifying SAMseq to account for asymmetry in the distribution of effect sizes when identifying differentially expressed genes
• Empirical Bayes analysis of RNA sequencing experiments with auxiliary information
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• No counts, no variance: allowing for loss of degrees of freedom when assessing biological variability from RNA-seq data

Cites work

• scientific article; zbMATH DE number 720689 (Why is no real title available?)
• A Direct Approach to False Discovery Rates
• Comment: ``Microarrays, empirical Bayes and the two-groups model
• False discovery control with p-value weighting
• Genome-wide significance levels and weighted hypothesis testing
• High-dimensional variable selection
• Simultaneous Testing of Grouped Hypotheses: Finding Needles in Multiple Haystacks
• Simultaneous inference: when should hypothesis testing problems be combined?

Describes a project that uses

Uses Software

• Bioconductor
• edgeR
• DEGseq
• BaySeq
• DEseq

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