MOTIVATION: Combining P-values from multiple statistical tests is a common exercise in bioinformatics. However, this procedure is non-trivial for dependent P-values. Here, we discuss an empirical adaptation of Brown's method (an extension of Fisher's method) for combining dependent P-values which is appropriate for the large and correlated datasets found in high-throughput biology. RESULTS: We show that the Empirical Brown's method (EBM) outperforms Fisher's method as well as alternative approaches for combining dependent P-values using both noisy simulated data and gene expression data from The Cancer Genome Atlas. AVAILABILITY AND IMPLEMENTATION: The Empirical Brown's method is available in Python, R, and MATLAB and can be obtained from https://github.com/IlyaLab/CombiningDependentPvalues UsingEBM The R code is also available as a Bioconductor package from https://www.bioconductor.org/packages/devel/bioc/html/EmpiricalBrownsMethod.html CONTACT: Theo.Knijnenburg@systemsbiology.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Combining P-values from multiple statistical tests is a common exercise in bioinformatics. However, this procedure is non-trivial for dependent P-values. Here, we discuss an empirical adaptation of Brown's method (an extension of Fisher's method) for combining dependent P-values which is appropriate for the large and correlated datasets found in high-throughput biology. RESULTS: We show that the Empirical Brown's method (EBM) outperforms Fisher's method as well as alternative approaches for combining dependent P-values using both noisy simulated data and gene expression data from The Cancer Genome Atlas. AVAILABILITY AND IMPLEMENTATION: The Empirical Brown's method is available in Python, R, and MATLAB and can be obtained from https://github.com/IlyaLab/CombiningDependentPvalues UsingEBM The R code is also available as a Bioconductor package from https://www.bioconductor.org/packages/devel/bioc/html/EmpiricalBrownsMethod.html CONTACT: Theo.Knijnenburg@systemsbiology.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Cameron W Brennan; Roel G W Verhaak; Aaron McKenna; Benito Campos; Houtan Noushmehr; Sofie R Salama; Siyuan Zheng; Debyani Chakravarty; J Zachary Sanborn; Samuel H Berman; Rameen Beroukhim; Brady Bernard; Chang-Jiun Wu; Giannicola Genovese; Ilya Shmulevich; Jill Barnholtz-Sloan; Lihua Zou; Rahulsimham Vegesna; Sachet A Shukla; Giovanni Ciriello; W K Yung; Wei Zhang; Carrie Sougnez; Tom Mikkelsen; Kenneth Aldape; Darell D Bigner; Erwin G Van Meir; Michael Prados; Andrew Sloan; Keith L Black; Jennifer Eschbacher; Gaetano Finocchiaro; William Friedman; David W Andrews; Abhijit Guha; Mary Iacocca; Brian P O'Neill; Greg Foltz; Jerome Myers; Daniel J Weisenberger; Robert Penny; Raju Kucherlapati; Charles M Perou; D Neil Hayes; Richard Gibbs; Marco Marra; Gordon B Mills; Eric Lander; Paul Spellman; Richard Wilson; Chris Sander; John Weinstein; Matthew Meyerson; Stacey Gabriel; Peter W Laird; David Haussler; Gad Getz; Lynda Chin Journal: Cell Date: 2013-10-10 Impact factor: 41.582
Authors: Goncalo R Abecasis; Adam Auton; Lisa D Brooks; Mark A DePristo; Richard M Durbin; Robert E Handsaker; Hyun Min Kang; Gabor T Marth; Gil A McVean Journal: Nature Date: 2012-11-01 Impact factor: 49.962
Authors: Carl F Schaefer; Kira Anthony; Shiva Krupa; Jeffrey Buchoff; Matthew Day; Timo Hannay; Kenneth H Buetow Journal: Nucleic Acids Res Date: 2008-10-02 Impact factor: 16.971
Authors: Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi-Moussavi; Pouya Kheradpour; Zhizhuo Zhang; Jianrong Wang; Michael J Ziller; Viren Amin; John W Whitaker; Matthew D Schultz; Lucas D Ward; Abhishek Sarkar; Gerald Quon; Richard S Sandstrom; Matthew L Eaton; Yi-Chieh Wu; Andreas R Pfenning; Xinchen Wang; Melina Claussnitzer; Yaping Liu; Cristian Coarfa; R Alan Harris; Noam Shoresh; Charles B Epstein; Elizabeta Gjoneska; Danny Leung; Wei Xie; R David Hawkins; Ryan Lister; Chibo Hong; Philippe Gascard; Andrew J Mungall; Richard Moore; Eric Chuah; Angela Tam; Theresa K Canfield; R Scott Hansen; Rajinder Kaul; Peter J Sabo; Mukul S Bansal; Annaick Carles; Jesse R Dixon; Kai-How Farh; Soheil Feizi; Rosa Karlic; Ah-Ram Kim; Ashwinikumar Kulkarni; Daofeng Li; Rebecca Lowdon; GiNell Elliott; Tim R Mercer; Shane J Neph; Vitor Onuchic; Paz Polak; Nisha Rajagopal; Pradipta Ray; Richard C Sallari; Kyle T Siebenthall; Nicholas A Sinnott-Armstrong; Michael Stevens; Robert E Thurman; Jie Wu; Bo Zhang; Xin Zhou; Arthur E Beaudet; Laurie A Boyer; Philip L De Jager; Peggy J Farnham; Susan J Fisher; David Haussler; Steven J M Jones; Wei Li; Marco A Marra; Michael T McManus; Shamil Sunyaev; James A Thomson; Thea D Tlsty; Li-Huei Tsai; Wei Wang; Robert A Waterland; Michael Q Zhang; Lisa H Chadwick; Bradley E Bernstein; Joseph F Costello; Joseph R Ecker; Martin Hirst; Alexander Meissner; Aleksandar Milosavljevic; Bing Ren; John A Stamatoyannopoulos; Ting Wang; Manolis Kellis Journal: Nature Date: 2015-02-19 Impact factor: 69.504
Authors: Steve Hoffmann; Karol Szafranski; Philip Dammann; Arne Sahm; Matthias Platzer; Philipp Koch; Yoshiyuki Henning; Martin Bens; Marco Groth; Hynek Burda; Sabine Begall; Saskia Ting; Moritz Goetz; Paul Van Daele; Magdalena Staniszewska; Jasmin Mona Klose; Pedro Fragoso Costa Journal: Elife Date: 2021-03-16 Impact factor: 8.140
Authors: Andrea Rubio-Ponce; Iván Ballesteros; Juan A Quintana; Guiomar Solanas; Salvador A Benitah; Andrés Hidalgo; Fátima Sánchez-Cabo Journal: NAR Genom Bioinform Date: 2021-04-26
Authors: Martin J Lan; Mina M Rizk; Spiro P Pantazatos; Harry Rubin-Falcone; Jeffrey M Miller; M Elizabeth Sublette; Maria A Oquendo; John G Keilp; J John Mann Journal: Depress Anxiety Date: 2019-03-21 Impact factor: 6.505
Authors: Omar El Charif; Brandon Mapes; Matthew R Trendowski; Heather E Wheeler; Claudia Wing; Paul C Dinh; Robert D Frisina; Darren R Feldman; Robert J Hamilton; David J Vaughn; Chunkit Fung; Christian Kollmannsberger; Taisei Mushiroda; Michiaki Kubo; Eric R Gamazon; Nancy J Cox; Robert Huddart; Shirin Ardeshir-Rouhani-Fard; Patrick Monahan; Sophie D Fossa; Lawrence H Einhorn; Lois B Travis; M Eileen Dolan Journal: Clin Cancer Res Date: 2019-04-05 Impact factor: 12.531
Authors: Hong Dang; Deepika Polineni; Rhonda G Pace; Jaclyn R Stonebraker; Harriet Corvol; Garry R Cutting; Mitchell L Drumm; Lisa J Strug; Wanda K O'Neal; Michael R Knowles Journal: PLoS One Date: 2020-11-30 Impact factor: 3.240
Authors: Sanne Arjaans; Brandie D Wagner; Peter M Mourani; Erica W Mandell; Brenda B Poindexter; Rolf M F Berger; Steven H Abman Journal: Am J Physiol Lung Cell Mol Physiol Date: 2020-01-22 Impact factor: 5.464