Data-driven hypothesis weighting increases detection power in genome-scale multiple testing

Nature Methods
Nikolaos IgnatiadisWolfgang Huber

Abstract

Hypothesis weighting improves the power of large-scale multiple testing. We describe independent hypothesis weighting (IHW), a method that assigns weights using covariates independent of the P-values under the null hypothesis but informative of each test's power or prior probability of the null hypothesis (http://www.bioconductor.org/packages/IHW). IHW increases power while controlling the false discovery rate and is a practical approach to discovering associations in genomics, high-throughput biology and other large data sets.

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Citations

Jun 17, 2016·Genome Biology·Jonathan CairnsMikhail Spivakov
Feb 27, 2018·Nature Methods·Charlotte Soneson, Mark D Robinson
Apr 17, 2018·Bioinformatics·H Robert Frost
Feb 23, 2018·Molecular Systems Biology·Benedikt RauscherMichael Boutros
Sep 19, 2018·Nature Microbiology·Aartjan J W Te VelthuisErvin Fodor
Nov 23, 2019·The Journal of Biological Chemistry·Darren M BlackburnVahab D Soleimani
Aug 24, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Paul R JohnstonJens Rolff
May 6, 2020·Biometrical Journal. Biometrische Zeitschrift·Xiongzhi ChenSanat K Sarkar
May 13, 2020·PloS One·Vladimir MashanovDaniel Janies
Mar 6, 2019·Journal of Bacteriology·Courtney K EllisonYves V Brun
Oct 24, 2017·Journal of Comparative Physiology. A, Neuroethology, Sensory, Neural, and Behavioral Physiology·G Troy SmithDouglas B Rusch
Mar 28, 2019·The Journal of Experimental Medicine·Nour J AbdulhayVijay G Sankaran
Aug 3, 2019·Genes & Development·Federico ComoglioGioacchino Natoli
Mar 12, 2020·Genome Biology and Evolution·Claire BurnyChristian Schlötterer
Aug 8, 2019·Pflügers Archiv : European journal of physiology·Anne SteglichVladimir T Todorov
Dec 15, 2019·International Journal of Molecular Sciences·Joan Castells-BallesterSabine Strahl
Jun 28, 2020·Leukemia·Patrizia JensenStefan Fröhling
Jul 6, 2020·Nucleic Acids Research·Jennifer V GerbrachtNiels H Gehring
Jan 9, 2019·Nature Genetics·Khelifa ArabChristof Niehrs
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Apr 8, 2020·Acta Crystallographica. Section D, Structural Biology·Maximilian BeckersCarsten Sachse
Apr 12, 2017·Nature Biotechnology·Leonardo Collado-TorresJeffrey T Leek

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Methods Mentioned

BETA
RNA-seq
ChIP-seq

Software Mentioned

IHW

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