A field-wide assessment of differential expression profiling by high-throughput sequencing reveals widespread bias

Taavi Päll, Hannes Luidalepp, Tanel Tenson and Ülo Maiväli

PLOS Biology, 2023, vol. 21, issue 3, 1-27

Abstract: We assess inferential quality in the field of differential expression profiling by high-throughput sequencing (HT-seq) based on analysis of datasets submitted from 2008 to 2020 to the NCBI GEO data repository. We take advantage of the parallel differential expression testing over thousands of genes, whereby each experiment leads to a large set of p-values, the distribution of which can indicate the validity of assumptions behind the test. From a well-behaved p-value set π0, the fraction of genes that are not differentially expressed can be estimated. We found that only 25% of experiments resulted in theoretically expected p-value histogram shapes, although there is a marked improvement over time. Uniform p-value histogram shapes, indicative of

Date: 2023
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pbio00:3002007

DOI: 10.1371/journal.pbio.3002007

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