Cargando…

Inflated false discovery rate due to volcano plots: problem and solutions

MOTIVATION: Volcano 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 [Formula: see text]-value and...

Descripción completa

Detalles Bibliográficos
Autores principales:	Ebrahimpoor, Mitra, Goeman, Jelle J
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2021
Materias:	Method Review
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8425469/ https://www.ncbi.nlm.nih.gov/pubmed/33758907 http://dx.doi.org/10.1093/bib/bbab053

Ejemplares similares

Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery
por: Köster, Johannes, et al.
Publicado: (2020)

Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril
por: Wisotsky, Sadie R, et al.
Publicado: (2020)

Machine learning meets volcano plots: computational discovery of cross-coupling catalysts
por: Meyer, Benjamin, et al.
Publicado: (2018)

Simultaneous Enrichment Analysis of all Possible Gene-sets: Unifying Self-Contained and Competitive Methods
por: Ebrahimpoor, Mitra, et al.
Publicado: (2019)

Volcano plots in hydrogen electrocatalysis – uses and abuses
por: Quaino, Paola, et al.
Publicado: (2014)

Pathway testing for longitudinal metabolomics
por: Ebrahimpoor, Mitra, et al.
Publicado: (2021)

Power, false discovery rate and Winner’s Curse in eQTL studies
por: Huang, Qin Qin, et al.
Publicado: (2018)

Data-powered augmented volcano plots for homogeneous catalysis
por: Wodrich, Matthew D., et al.
Publicado: (2020)

Robust volcano plot: identification of differential metabolites in the presence of outliers
por: Kumar, Nishith, et al.
Publicado: (2018)

Estimating the local false discovery rate via a bootstrap solution to the reference class problem
por: Abbas-Aghababazadeh, Farnoosh, et al.
Publicado: (2018)

stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage
por: Van den Berge, Koen, et al.
Publicado: (2017)

Accessing and predicting the kinetic profiles of homogeneous catalysts from volcano plots
por: Wodrich, Matthew D., et al.
Publicado: (2016)

A scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control
por: van Dyk, Ewald, et al.
Publicado: (2013)

False discovery rates in spectral identification
por: Jeong, Kyowon, et al.
Publicado: (2012)

Linear scaling relationships and volcano plots in homogeneous catalysis – revisiting the Suzuki reaction
por: Busch, Michael, et al.
Publicado: (2015)

Two-Stage Inflation as a Solution to the Initial Condition Problem of Hybrid Inflation
por: Panagiotakopoulos, C., et al.
Publicado: (1997)

Uncovering the Activity of Alkaline Earth Metal Hydrogenation Catalysis Through Molecular Volcano Plots
por: Das, Shubhajit, et al.
Publicado: (2021)

cn.FARMS: a latent variable model to detect copy number variations in microarray data with a low false discovery rate
por: Clevert, Djork-Arné, et al.
Publicado: (2011)

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate
por: Klambauer, Günter, et al.
Publicado: (2012)

Within-forest stand (or formation, or plot) and between-forest stand (or formation, or plot) biodiversity indices
por: Kitikidou, Kyriaki, et al.
Publicado: (2022)

Inflation, inflation uncertainty and the economic growth nexus: An impact study of South Africa
por: Mandeya, Shelton Masimba Tafadzwa, et al.
Publicado: (2021)

VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots
por: Goedhart, Joachim, et al.
Publicado: (2020)

Stairway Plot 2: demographic history inference with folded SNP frequency spectra
por: Liu, Xiaoming, et al.
Publicado: (2020)

Controlling the Rate of GWAS False Discoveries
por: Brzyski, Damian, et al.
Publicado: (2017)

An investigation of the false discovery rate and the misinterpretation of p-values
por: Colquhoun, David
Publicado: (2014)

The Gravitational Wave Background and Higgs False Vacuum Inflation
por: Masina, Isabella
Publicado: (2014)

Controlling bias and inflation in epigenome- and transcriptome-wide association studies using the empirical null distribution
por: van Iterson, Maarten, et al.
Publicado: (2017)

Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
por: Van den Berge, Koen, et al.
Publicado: (2018)

mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis
por: Zeng, Yanyan, et al.
Publicado: (2022)

Plea for routinely presenting prediction intervals in meta-analysis
por: IntHout, Joanna, et al.
Publicado: (2016)

False discovery rates: a new deal
por: Stephens, Matthew
Publicado: (2017)

4497 Accessible False Discovery Rate Computation
por: Hollister, Megan C, et al.
Publicado: (2020)

The functional false discovery rate with applications to genomics
por: Chen, Xiongzhi, et al.
Publicado: (2019)

Allele dynamics plots for the study of evolutionary dynamics in viral populations
por: Steinbrück, Lars, et al.
Publicado: (2011)

Inflation rate modeling: Adaptive neuro-fuzzy inference system approach and particle swarm optimization algorithm (ANFIS-PSO)
por: Robati, Fateme Nazari, et al.
Publicado: (2020)

Volcano Plots Emerge from a Sea of Nonaqueous Solvents: The Law of Matching Water Affinities Extends to All Solvents
por: Mazzini, Virginia, et al.
Publicado: (2018)

Symmetry Breaking and False Vacuum Decay after Hybrid Inflation
por: García-Bellido, J, et al.
Publicado: (2002)

Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database
por: Tung, Chi-Hua, et al.
Publicado: (2007)

Improving the visualization, interpretation and analysis of two-sample summary data Mendelian randomization via the Radial plot and Radial regression
por: Bowden, Jack, et al.
Publicado: (2018)

On the equivalence of one‐inflated zero‐truncated and zero‐truncated one‐inflated count data likelihoods
por: Böhning, Dankmar
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_640o57b2ckd8im6fgbr8fdcpmq