ArticleBMC bioinformatics2017
A statistical method for the conservative adjustment of false discovery rate (q-value).
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
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- High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Evolutionary applications · 2022Article
- Diet and erythrocyte metal concentrations in early pregnancy-cross-sectional analysis in Project Viva.The American journal of clinical nutrition · 2021Article
- A genetic interaction of NRXN2 with GABRE, SYT1 and CASK in migraine patients: a case-control study.The journal of headache and pain · 2021Article
- Mitochondrial Functionality in Male Fertility: From Spermatogenesis to Fertilization.Antioxidants (Basel, Switzerland) · 2021Review
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Abstract
backgroundq-value is a widely used statistical method for estimating false discovery rate (FDR), which is a conventional significance measure in the analysis of genome-wide expression data. q-value is a random variable and it may underestimate FDR in practice. An underestimated FDR can lead to unexpected false discoveries in the follow-up validation experiments. This issue has not been well addressed in literature, especially in the situation when the permutation procedure is necessary for p-value calculation.
resultsWe proposed a statistical method for the conservative adjustment of q-value. In practice, it is usually necessary to calculate p-value by a permutation procedure. This was also considered in our adjustment method. We used simulation data as well as experimental microarray or sequencing data to illustrate the usefulness of our method.
conclusionsThe conservativeness of our approach has been mathematically confirmed in this study. We have demonstrated the importance of conservative adjustment of q-value, particularly in the situation that the proportion of differentially expressed genes is small or the overall differential expression signal is weak.
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