Estimating the local false discovery rate via a bootstrap solution to the reference class problem

PloS One
Farnoosh Abbas-AghababazadehDavid R Bickel

Abstract

Methods of estimating the local false discovery rate (LFDR) have been applied to different types of datasets such as high-throughput biological data, diffusion tensor imaging (DTI), and genome-wide association (GWA) studies. We present a model for LFDR estimation that incorporates a covariate into each test. Incorporating the covariates may improve the performance of testing procedures, because it contains additional information based on the biological context of the corresponding test. This method provides different estimates depending on a tuning parameter. We estimate the optimal value of that parameter by choosing the one that minimizes the estimated LFDR resulting from the bias and variance in a bootstrap approach. This estimation method is called an adaptive reference class (ARC) method. In this study, we consider the performance of ARC method under certain assumptions on the prior probability of each hypothesis test as a function of the covariate. We prove that, under these assumptions, the ARC method has a mean squared error asymptotically no greater than that of the other method where the entire set of hypotheses is used and assuming a large covariate effect. In addition, we conduct a simulation study to evaluate the p...Continue Reading

References

Jul 26, 2002·Briefings in Bioinformatics·Cathryn M Lewis
Apr 23, 2004·Neuroradiology·P C SundgrenR Welsh
Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang
May 6, 2005·Cortex; a Journal Devoted to the Study of the Nervous System and Behavior·Gayle K DeutschBrian Wandell
May 21, 2005·Magnetic Resonance in Medicine : Official Journal of the Society of Magnetic Resonance in Medicine·Armin SchwartzmanJonathan E Taylor
Dec 22, 2005·Bioinformatics·Alexander PlonerYudi Pawitan
Jun 8, 2007·Nature·UNKNOWN Wellcome Trust Case Control Consortium
Dec 20, 2007·American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics·Edwin J C G van den Oord
May 8, 2009·Bioinformatics·József BukszárEdwin J C G van den Oord
Dec 17, 2009·Nature Biotechnology·William S Noble
Mar 3, 2010·Molecular Psychiatry·D E AdkinsE J C G van den Oord
Aug 17, 2010·Statistical Science : a Review Journal of the Institute of Mathematical Statistics·Kathryn Roeder, Larry Wasserman
Sep 21, 2011·Journal of the American Statistical Association·James X HuHarrison H Zhou
May 25, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ye YangDavid R Bickel
Apr 9, 2014·Bioinformatics·Rong W ZablockiWesley K Thompson
Aug 17, 2018·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ali Karimnezhad, David R Bickel

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