Results 1  10
of
337
A direct approach to false discovery rates
, 2002
"... Summary. Multiplehypothesis testing involves guarding against much more complicated errors than singlehypothesis testing. Whereas we typically control the type I error rate for a singlehypothesis test, a compound error rate is controlled for multiplehypothesis tests. For example, controlling the ..."
Abstract

Cited by 775 (14 self)
 Add to MetaCart
(Show Context)
Summary. Multiplehypothesis testing involves guarding against much more complicated errors than singlehypothesis testing. Whereas we typically control the type I error rate for a singlehypothesis test, a compound error rate is controlled for multiplehypothesis tests. For example, controlling the false discovery rate FDR traditionally involves intricate sequential pvalue rejection methods based on the observed data. Whereas a sequential pvalue method fixes the error rate and estimates its corresponding rejection region, we propose the opposite approach—we fix the rejection region and then estimate its corresponding error rate. This new approach offers increased applicability, accuracy and power. We apply the methodology to both the positive false discovery rate pFDR and FDR, and provide evidence for its benefits. It is shown that pFDR is probably the quantity of interest over FDR. Also discussed is the calculation of the qvalue, the pFDR analogue of the pvalue, which eliminates the need to set the error rate beforehand as is traditionally done. Some simple numerical examples are presented that show that this new approach can yield an increase of over eight times in power compared with the Benjamini–Hochberg FDR method.
Empirical Bayes Analysis of a Microarray Experiment
 Journal of the American Statistical Association
, 2001
"... Microarrays are a novel technology that facilitates the simultaneous measurement of thousands of gene expression levels. A typical microarray experiment can produce millions of data points, raising serious problems of data reduction, and simultaneous inference. We consider one such experiment in whi ..."
Abstract

Cited by 492 (20 self)
 Add to MetaCart
Microarrays are a novel technology that facilitates the simultaneous measurement of thousands of gene expression levels. A typical microarray experiment can produce millions of data points, raising serious problems of data reduction, and simultaneous inference. We consider one such experiment in which oligonucleotide arrays were employed to assess the genetic effects of ionizing radiation on seven thousand human genes. A simple nonparametric empirical Bayes model is introduced, which is used to guide the ef � cient reduction of the data to a single summary statistic per gene, and also to make simultaneous inferences concerning which genes were affected by the radiation. Although our focus is on one speci � c experiment, the proposed methods can be applied quite generally. The empirical Bayes inferences are closely related to the frequentist false discovery rate (FDR) criterion. 1.
Largescale simultaneous hypothesis testing: the choice of a null hypothesis
 JASA
, 2004
"... Current scientific techniques in genomics and image processing routinely produce hypothesis testing problems with hundreds or thousands of cases to consider simultaneously. This poses new difficulties for the statistician, but also opens new opportunities. In particular it allows empirical estimatio ..."
Abstract

Cited by 301 (15 self)
 Add to MetaCart
Current scientific techniques in genomics and image processing routinely produce hypothesis testing problems with hundreds or thousands of cases to consider simultaneously. This poses new difficulties for the statistician, but also opens new opportunities. In particular it allows empirical estimation of an appropriate null hypothesis. The empirical null may be considerably more dispersed than the usual theoretical null distribution that would be used for any one case considered separately. An empirical Bayes analysis plan for this situation is developed, using a local version of the false discovery rate to examine the inference issues. Two genomics problems are used as examples to show the importance of correctly choosing the null hypothesis. Key Words: local false discovery rate, empirical Bayes, microarray analysis, empirical null hypothesis, unobserved covariates
Identifying differentially expressed genes using false discovery rate controlling procedures
 BIOINFORMATICS 19: 368–375
, 2003
"... Motivation: DNA microarrays have recently been used for the purpose of monitoring expression levels of thousands of genes simultaneously and identifying those genes that are differentially expressed. The probability that a false identification (type I error) is committed can increase sharply when th ..."
Abstract

Cited by 233 (2 self)
 Add to MetaCart
Motivation: DNA microarrays have recently been used for the purpose of monitoring expression levels of thousands of genes simultaneously and identifying those genes that are differentially expressed. The probability that a false identification (type I error) is committed can increase sharply when the number of tested genes gets large. Correlation between the test statistics attributed to gene coregulation and dependency in the measurement errors of the gene expression levels further complicates the problem. In this paper we address this very large multiplicity problem by adopting the false discovery rate (FDR) controlling approach. In order to address the dependency problem, we present three resamplingbased FDR controlling procedures, that account for the test statistics distribution, and compare their performance to that of the naïve application of the linear stepup procedure in Benjamini and Hochberg (1995). The procedures are studied using simulated microarray data, and their performance is examined relative to their ease of implementation. Results: Comparative simulation analysis shows that all four FDR controlling procedures control the FDR at the desired level, and retain substantially more power then the familywise error rate controlling procedures. In terms of power, using resampling of the marginal distribution of each test statistics substantially improves the performance over the naïve one. The highest power is achieved, at the expense of a more sophisticated algorithm, by the resamplingbased procedures that resample the joint distribution of the test statistics and estimate the level of FDR control.
ResamplingBased Multiple Testing for Microarray Data Analysis
, 2003
"... The burgeoning field of genomics has revived interest in multiple testing procedures by raising new methodological and computational challenges. For example, microarray experiments generate large multiplicity problems in which thousands of hypotheses are tested simultaneously. In their 1993 book, We ..."
Abstract

Cited by 145 (3 self)
 Add to MetaCart
The burgeoning field of genomics has revived interest in multiple testing procedures by raising new methodological and computational challenges. For example, microarray experiments generate large multiplicity problems in which thousands of hypotheses are tested simultaneously. In their 1993 book, Westfall & Young propose resamplingbased pvalue adjustment procedures which are highly relevant to microarray experiments. This article discusses different criteria for error control in resamplingbased multiple testing, including (a) the family wise error rate of Westfall & Young (1993) and (b) the false discovery rate developed by Benjamini & Hochberg (1995), both from a frequentist viewpoint; and (c) the positive false discovery rate of Storey (2002), which has a Bayesian motivation. We also introduce our recently developed fast algorithm for implementing the minP adjustment to control familywise error rate. Adjusted pvalues for different approaches are applied to gene expression data from two recently published microarray studies. The properties of these procedures for multiple testing are compared.
A stochastic process approach to False discovery rates
, 2001
"... This paper extends the theory of false discovery rates (FDR) pioneered by Benjamini and Hochberg (1995). We develop a framework in which the False Discovery Proportion (FDP) – the number of false rejections divided by the number of rejections – is treated as a stochastic process. After obtaining th ..."
Abstract

Cited by 132 (6 self)
 Add to MetaCart
This paper extends the theory of false discovery rates (FDR) pioneered by Benjamini and Hochberg (1995). We develop a framework in which the False Discovery Proportion (FDP) – the number of false rejections divided by the number of rejections – is treated as a stochastic process. After obtaining the limiting distribution of the process, we demonstrate the validitiy of a class of procedures for controlling the False Discovery Rate (the expected FDP). We construct a confidence envelope for the whole FDP process. From these envelopes we derive confidence thresholds, for controlling the quantiles of the distribution of the FDP as well as controlling the number of false discoveries. We also
Posterior consistency of Dirichlet mixtures in density estimation
 Ann. Statist
, 1999
"... A Dirichlet mixture of normal densities is a useful choice for a prior distribution on densities in the problem of Bayesian density estimation. In the recent years, efficient Markov chain Monte Carlo method for the computation of the posterior distribution has been developed. The method has been app ..."
Abstract

Cited by 120 (21 self)
 Add to MetaCart
A Dirichlet mixture of normal densities is a useful choice for a prior distribution on densities in the problem of Bayesian density estimation. In the recent years, efficient Markov chain Monte Carlo method for the computation of the posterior distribution has been developed. The method has been applied to data arising from different fields of interest. The important issue of consistency was however left open. In this paper, we settle this issue in affirmative. 1. Introduction. Recent
An exploration of aspects of Bayesian multiple testing
 Journal of Statistical Planning and Inference
, 2005
"... There has been increased interest of late in the Bayesian approach to multiple testing (often called the multiple comparisons problem), motivated by the need to analyze DNA microarray data in which it is desired to learn which of potentially several thousand genes are activated by a particular stimu ..."
Abstract

Cited by 76 (12 self)
 Add to MetaCart
There has been increased interest of late in the Bayesian approach to multiple testing (often called the multiple comparisons problem), motivated by the need to analyze DNA microarray data in which it is desired to learn which of potentially several thousand genes are activated by a particular stimulus. We study the issue of prior specification for such multiple tests; computation of key posterior quantities; and useful ways to display these quantities. A decisiontheoretic approach is also considered.
False Discoveries in Mutual Fund Performance: Measuring Luck in Estimated Alphas
 Journal of Finance
, 2010
"... and SGF 2006 for their helpful comments. The first and second authors acknowledge ..."
Abstract

Cited by 65 (6 self)
 Add to MetaCart
and SGF 2006 for their helpful comments. The first and second authors acknowledge
Distributed detection in sensor networks with packet losses and finite capacity links
 IEEE Transactions on Signal Processing
, 2006
"... We consider a multiobject detection problem over a sensor network (SNET) with limited range multimodal sensors. Limited range sensing environment arises in a sensing field prone to signal attenuation and path losses. The general problem complements the widely considered decentralized detection pro ..."
Abstract

Cited by 64 (5 self)
 Add to MetaCart
(Show Context)
We consider a multiobject detection problem over a sensor network (SNET) with limited range multimodal sensors. Limited range sensing environment arises in a sensing field prone to signal attenuation and path losses. The general problem complements the widely considered decentralized detection problem where all sensors observe the same object. In this paper we develop a distributed detection approach based on recent development of the false discovery rate (FDR) and the associated BH test procedure. The BH procedure is based on rank ordering of scalar test statistics. We first develop scalar test statistics for multidimensional data to handle multimodal sensor observations and establish its optimality in terms of the BH procedure. We then propose a distributed algorithm in the ideal case of infinite attenuation for identification of sensors that are in the immediate vicinity of an object. We demonstrate communication message scalability to large SNETs by showing that the upper bound on the communication message complexity scales linearly with the number of sensors that are in the vicinity of objects and is independent of the total number of sensors in the SNET. This brings forth an important principle for evaluating the performance of an SNET, namely, the need for scalability of communications and performance with respect to the number of objects or events in an SNET irrespective of the network size. We then account for finite attenuation by modeling sensor observations as corrupted by uncertain interference arising from distant objects and developing robust extensions to our idealized distributed scheme. The robustness properties ensure that both the error performance and communication message complexity degrade gracefully with interference. 1