在半合成 RNA-seq 数据模拟中忽略归一化的影响会产生人为假阳性结果

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2024-10-30 DOI:10.1186/s13059-024-03231-9

Boris P. Hejblum, Kalidou Ba, Rodolphe Thiébaut, Denis Agniel

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引用次数: 0

摘要

最近的一项研究报告称，流行的差异表达分析方法在分析大量群体样本时会出现夸大的假阳性。我们重现了差异表达分析的模拟结果，并发现了数据生成过程中的一个注意事项。由于数据不是在零假设下真实生成的，导致基准方法的比较结果不正确。我们提供了修正后的模拟结果，证明了 dearseq 的良好性能，并反驳了之前研究中提出的 Wilcoxon 秩和检验的优越性。

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Neglecting the impact of normalization in semi-synthetic RNA-seq data simulations generates artificial false positives

A recent study reported exaggerated false positives by popular differential expression methods when analyzing large population samples. We reproduce the differential expression analysis simulation results and identify a caveat in the data generation process. Data not truly generated under the null hypothesis led to incorrect comparisons of benchmark methods. We provide corrected simulation results that demonstrate the good performance of dearseq and argue against the superiority of the Wilcoxon rank-sum test as suggested in the previous study.

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.