ArticleBriefings in bioinformatics2021
Inflated false discovery rate due to volcano plots: problem and solutions.
Article in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed.
- Not every gene is special: Modelling scale controls the false discovery rate when analysing high-throughput sequencing data.PLoS computational biology · 2026Article
- Spatially resolved lipids in a mouse brain model of globoid cell leukodystrophy via IR-MALDESI MSI and parallel reaction monitoring MSI.Analytical and bioanalytical chemistry · 2026Article
- Incorporating Scale Uncertainty into Differential Expression Analyses Using ALDEx2.Current protocols · 2026Article
- NBSR: a Negative Binomial Softmax Regression model for microRNA-seq data analysis.Biostatistics (Oxford, England) · 2026Article
- Metabolite biomarkers present in urine predict alterations in skeletal muscle associated with sarcopenia.Frontiers in aging · 2026Article
- ChromTag: an interactive R-shiny platform for analysis and visualization of CUT&Tag and ChIP-seq peak profiling data.Frontiers in bioinformatics · 2026Article
- Comparative proteomic analysis of Porphyromonas gingivalis challenged human dental pulp stem cells.Scientific reports · 2025Article
- Explicit Scale Simulation for analysis of RNA-sequencing count data with ALDEx2.NAR genomics and bioinformatics · 2025Article
- Replicability of bulk RNA-Seq differential expression and enrichment analysis results for small cohort sizes.PLoS computational biology · 2025Article
- Robust Cancer Biomarker Identification From Matched Transcriptomic Data Via Bootstrapped Regularized Conditional Logistic Regression.Cancer informatics · 2025Article
- Elucidating epigenetic landscape of gastric premalignant lesions through genome-wide mapping of 5-hydroxymethylcytosines: A 12-year median follow-up study.Clinical and translational medicine · 2024Article
- PRC1 Protein Subcomplexes Architecture: Focus on the Interplay between Distinct PCGF Subunits in Protein Interaction Networks.International journal of molecular sciences · 2024Article
- Statistical plots in oncologic imaging, a primer for neuroradiologists.The neuroradiology journal · 2024Review
- Combining Partial True Discovery Guarantee Procedures.Biometrical journal. Biometrische Zeitschrift · 2024Article
- Detection Algorithms for Simple Two-Group Comparisons Using Spontaneous Reporting Systems.Drug safety · 2024Review
- Fudging the volcano-plot without dredging the data.Nature communications · 2024Article
- Proteomic profiling identifies SPP1 associated with rapidly progressive interstitial lung disease in anti-MDA5-positive dermatomyositis.Arthritis research & therapy · 2024Article
- Exaggerated false positives by popular differential expression methods when analyzing human population samples.Genome biology · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationVolcano plots are used to select the most interesting discoveries when too many discoveries remain after application of Benjamini-Hochberg's procedure (BH). The volcano plot suggests a double filtering procedure that selects features with both small adjusted $P$-value and large estimated effect size. Despite its popularity, this type of selection overlooks the fact that BH does not guarantee error control over filtered subsets of discoveries. Therefore the selected subset of features may include an inflated number of false discoveries.
resultsIn this paper, we illustrate the substantially inflated type I error rate of volcano plot selection with simulation experiments and RNA-seq data. In particular, we show that the feature with the largest estimated effect is a very likely false positive result. Next, we investigate two alternative approaches for multiple testing with double filtering that do not inflate the false discovery rate. Our procedure is implemented in an interactive web application and is publicly available.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.