Comparisons of estimators of the number of true null hypotheses and adaptive FDR procedures in multiplicity testing

Many exploratory studies such as microarray experiments require the simultaneous comparison of hundreds or thousands of genes. It is common to see that most genes in many microarray experiments are not expected to be differentially expressed. Under such a setting, a procedure that is designed to control the false discovery rate (FDR) is aimed at identifying as many potential differentially expressed genes as possible. The usual FDR controlling procedure is constructed based on the number of hypotheses. However, it can become very conservative when some of the alternative hypotheses are expected to be true. The power of a controlling procedure can be improved if the number of true null hypotheses (m ₀) instead of the number of hypotheses is incorporated in the procedure [Y. Benjamini and Y. Hochberg, On the adaptive control of the false discovery rate in multiple testing with independent statistics, J. Edu. Behav. Statist. 25(2000), pp. 60–83]. Nevertheless, m ₀ is unknown, and has to be estimated. The objective of this article is to evaluate some existing estimators of m ₀ and discuss the feasibility of these estimators in incorporating into FDR controlling procedures under various experimental settings. The results of simulations can help the investigator to choose an appropriate procedure to meet the requirement of the study.     

A new procedure for variance estimation in simple random sampling using auxiliary information

In this article we have envisaged an efficient generalized class of estimators for finite population variance of the study variable in simple random sampling using information on an auxiliary variable. Asymptotic expressions of the bias and mean square error of the proposed class of estimators have been obtained. Asymptotic optimum estimator in the proposed class of estimators has been identified with its mean square error formula. We have shown that the proposed class of estimators is more efficient than the usual unbiased, difference, Das and Tripathi (Sankhya C 40:139–148, 1978), Isaki (J. Am. Stat. Assoc. 78:117–123, 1983), Singh et al. (Curr. Sci. 57:1331–1334, 1988), Upadhyaya and Singh (Vikram Math. J. 19:14–17, 1999b), Kadilar and Cingi (Appl. Math. Comput. 173:2, 1047–1059, 2006a) and other estimators/classes of estimators. In the support of the theoretically results we have given an empirical study.     

One- and two-sample Bayesian prediction intervals based on progressively Type-II censored data

In this article, one- and two-sample Bayesian prediction intervals based on progressively Type-II censored data are derived. For the illustration of the developed results, the exponential, Pareto, Weibull and Burr Type-XII models are used as examples. Some of the previous results in the literature such as Dunsmore (Technometrics 16:455–460, 1974), Nigm and Hamdy (Commun Stat Theory Methods 16:1761–1772, 1987), Nigm (Commun Stat Theory Methods 18:897–911, 1989), Al-Hussaini and Jaheen (Commun Stat Theory Methods 24:1829–1842, 1995), Al-Hussaini (J Stat Plan Inference 79:79–91, 1999), Ali Mousa (J Stat Comput Simul 71: 163–181, 2001) and Ali Mousa and Jaheen (Stat Pap 43:587–593, 2002) can be achieved as special cases of our results. Finally, some numerical computations are presented for illustrating all the proposed inferential procedures.     

Efficient tests for one sample correlated binary data with applications

Four testing procedures are considered for testing the response rate of one sample correlated binary data with a cluster size of one or two, which often occurs in otolaryngologic and ophthalmologic studies. Although an asymptotic approach is often used for statistical inference, it is criticized for unsatisfactory type I error control in small sample settings. An alternative to the asymptotic approach is an unconditional approach. The first unconditional approach is the one based on estimation, also known as parametric bootstrap (Lee and Young in Stat Probab Lett 71(2):143–153, 2005). The other two unconditional approaches considered in this article are an approach based on maximization (Basu in J Am Stat Assoc 72(358):355–366, 1977), and an approach based on estimation and maximization (Lloyd in Biometrics 64(3):716–723, 2008a). These two unconditional approaches guarantee the test size and are generally more reliable than the asymptotic approach. We compare these four approaches in conjunction with a test proposed by Lee and Dubin (Stat Med 13(12):1241–1252, 1994) and a likelihood ratio test derived in this article, in regards to type I error rate and power for sample sizes from small to medium. An example from an otolaryngologic study is provided to illustrate the various testing procedures. The unconditional approach based on estimation and maximization using the test in Lee and Dubin (Stat Med 13(12):1241–1252, 1994) is preferable due to the power advantageous.     

Classical and Bayesian estimation of P(X<Y) using upper record values from Kumaraswamy’s distribution

In this paper, maximum likelihood and Bayesian approaches have been used to obtain the estimation of \(P(X<Y)\) based on a set of upper record values from Kumaraswamy distribution. The existence and uniqueness of the maximum likelihood estimates of the Kumaraswamy distribution parameters are obtained. Confidence intervals, exact and approximate, as well as Bayesian credible intervals are constructed. Bayes estimators have been developed under symmetric (squared error) and asymmetric (LINEX) loss functions using the conjugate and non informative prior distributions. The approximation forms of Lindley (Trabajos de Estadistica 3:281–288, 1980) and Tierney and Kadane (J Am Stat Assoc 81:82–86, 1986) are used for the Bayesian cases. Monte Carlo simulations are performed to compare the different proposed methods.     

On the strong convergence for weighted sums of ρ *-mixing random variables

A complete convergence result is obtained for weighted sums of identically distributed ρ ^*-mixing random variables with E|X ₁| ^α log(1 + |X ₁|) < ∞ for some 0 < α ≤ 2. This result partially extends the result of Sung (Stat Papers 52: 447–454, 2011) for negatively associated random variables to ρ ^*-mixing random variables. It also settles the open problem posed by Zhou et al. (J Inequal Appl, 2011, doi:10.1155/2011/157816).     

Influence diagnostics for Grubbs’s model with asymmetric heavy-tailed distributions

Grubbs’s model (Grubbs, Encycl Stat Sci 3:42–549, 1983) is used for comparing several measuring devices, and it is common to assume that the random terms have a normal (or symmetric) distribution. In this paper, we discuss the extension of this model to the class of scale mixtures of skew-normal distributions. Our results provide a useful generalization of the symmetric Grubbs’s model (Osorio et al., Comput Stat Data Anal, 53:1249–1263, 2009) and the asymmetric skew-normal model (Montenegro et al., Stat Pap 51:701–715, 2010). We discuss the EM algorithm for parameter estimation and the local influence method (Cook, J Royal Stat Soc Ser B, 48:133–169, 1986) for assessing the robustness of these parameter estimates under some usual perturbation schemes. The results and methods developed in this paper are illustrated with a numerical example.     

On tests of radial symmetry for bivariate copulas

The unique copula of a continuous random pair \((X,Y)\) is said to be radially symmetric if and only if it is also the copula of the pair \((-X,-Y)\) . This paper revisits the recently considered issue of testing for radial symmetry. Three rank-based statistics are proposed to this end which are asymptotically equivalent but simpler to compute than those of Bouzebda and Cherfi (J Stat Plan Inference 142:1262–1271, 2012). Their limiting null distribution and its approximation using the multiplier bootstrap are discussed. The finite-sample properties of the resulting tests are assessed via simulations. The asymptotic distribution of one of the test statistics is also computed under an arbitrary alternative, thereby correcting an error in the recent work of Dehgani et al. (Stat Pap 54:271–286, 2013).     

Evaluations of FDR-controlling procedures in multiple hypothesis testing

Many exploratory experiments such as DNA microarray or brain imaging require simultaneously comparisons of hundreds or thousands of hypotheses. Under such a setting, using the false discovery rate (FDR) as an overall Type I error is recommended (Benjamini and Hochberg in J. R. Stat. Soc. B 57:289–300, 1995). Many FDR controlling procedures have been proposed. However, when evaluating the performance of FDR-controlling procedures, researchers are often focused on the ability of procedures to control the FDR and to achieve high power. Meanwhile, under the multiple hypotheses, it may be also likely to commit a false non-discovery or fail to claim a true non-significance. In addition, various experimental parameters such as the number of hypotheses, the proportion of the number of true null hypotheses to the number of hypotheses, the samples size and the correlation structure may affect the performance of FDR controlling procedures. The purpose of this paper is to illustrate the performance of some existing FDR controlling procedures in terms of four indices, i.e., the FDR, the false non-discovery rate, the sensitivity and the specificity. Analytical results of these indices for the FDR controlling procedures are derived. Simulations are also performed to evaluate the performance of controlling procedures in terms of these indices under various experimental parameters. The result can be used to summarize as a guidance for practitioners to properly choose a FDR controlling procedure.     

A clarifying comparison of methods for controlling the false discovery rate

Traditional multiple hypothesis testing procedures fix an error rate and determine the corresponding rejection region. In 2002 Storey proposed a fixed rejection region procedure and showed numerically that it can gain more power than the fixed error rate procedure of Benjamini and Hochberg while controlling the same false discovery rate (FDR). In this paper it is proved that when the number of alternatives is small compared to the total number of hypotheses, Storey's method can be less powerful than that of Benjamini and Hochberg. Moreover, the two procedures are compared by setting them to produce the same FDR. The difference in power between Storey's procedure and that of Benjamini and Hochberg is near zero when the distance between the null and alternative distributions is large, but Benjamini and Hochberg's procedure becomes more powerful as the distance decreases. It is shown that modifying the Benjamini and Hochberg procedure to incorporate an estimate of the proportion of true null hypotheses as proposed by Black gives a procedure with superior power.     

Consistency of the likelihood depth estimator for the correlation coefficient

Denecke and Müller (CSDA 55:2724–2738, 2011) presented an estimator for the correlation coefficient based on likelihood depth for Gaussian copula and Denecke and Müller (J Stat Planning Inference 142: 2501–2517, 2012) proved a theorem about the consistency of general estimators based on data depth using uniform convergence of the depth measure. In this article, the uniform convergence of the depth measure for correlation is shown so that consistency of the correlation estimator based on depth can be concluded. The uniform convergence is shown with the help of the extension of the Glivenko-Cantelli Lemma by Vapnik- C? ervonenkis classes.     

Online signal extraction by robust regression in moving windows with data-adaptive width selection

Online (also ‘real-time’ or ‘sequential’) signal extraction from noisy and outlier-interfered data streams is a basic but challenging goal. Fitting a robust Repeated Median (Siegel in Biometrika 69:242–244, 1982) regression line in a moving time window has turned out to be a promising approach (Davies et al. in J. Stat. Plan. Inference 122:65–78, 2004; Gather et al. in Comput. Stat. 21:33–51, 2006; Schettlinger et al. in Biomed. Eng. 51:49–56, 2006). The level of the regression line at the rightmost window position, which equates to the current time point in an online application, is then used for signal extraction. However, the choice of the window width has a large impact on the signal extraction, and it is impossible to predetermine an optimal fixed window width for data streams which exhibit signal changes like level shifts and sudden trend changes. We therefore propose a robust test procedure for the online detection of such signal changes. An algorithm including the test allows for online window width adaption, meaning that the window width is chosen w.r.t. the current data situation at each time point. Comparison studies show that our new procedure outperforms an existing Repeated Median filter with automatic window width selection (Schettlinger et al. in Int. J. Adapt. Control Signal Process. 24:346–362, 2010).     

Approximate MLEs for the location and scale parameters of the skew logistic distribution

Azzalini (Scand J Stat 12:171–178, 1985) provided a methodology to introduce skewness in a normal distribution. Using the same method of Azzalini (1985), the skew logistic distribution can be easily obtained by introducing skewness to the logistic distribution. For the skew logistic distribution, the likelihood equations do not provide explicit solutions for the location and scale parameters. We present a simple method of deriving explicit estimators by approximating the likelihood equations appropriately. We examine numerically the bias and variance of these estimators and show that these estimators are as efficient as the maximum likelihood estimators (MLEs). The coverage probabilities of the pivotal quantities (for location and scale parameters) based on asymptotic normality are shown to be unsatisfactory, especially when the effective sample size is small. To improve the coverage probabilities and for constructing confidence intervals, we suggest the use of simulated percentage points. Finally, we present a numerical example to illustrate the methods of inference developed here.     

Robust parameter estimation for the Ornstein–Uhlenbeck process

In this paper, we derive elementary M- and optimally robust asymptotic linear (AL)-estimates for the parameters of an Ornstein–Uhlenbeck process. Simulation and estimation of the process are already well-studied, see Iacus (Simulation and inference for stochastic differential equations. Springer, New York, 2008). However, in order to protect against outliers and deviations from the ideal law the formulation of suitable neighborhood models and a corresponding robustification of the estimators are necessary. As a measure of robustness, we consider the maximum asymptotic mean square error (maxasyMSE), which is determined by the influence curve (IC) of AL estimates. The IC represents the standardized influence of an individual observation on the estimator given the past. In a first step, we extend the method of M-estimation from Huber (Robust statistics. Wiley, New York, 1981). In a second step, we apply the general theory based on local asymptotic normality, AL estimates, and shrinking neighborhoods due to Kohl et?al. (Stat Methods Appl 19:333–354, 2010), Rieder (Robust asymptotic statistics. Springer, New York, 1994), Rieder (2003), and Staab (1984). This leads to optimally robust ICs whose graph exhibits surprising behavior. In the end, we discuss the estimator construction, i.e. the problem of constructing an estimator from the family of optimal ICs. Therefore we carry out in our context the One-Step construction dating back to LeCam (Asymptotic methods in statistical decision theory. Springer, New York, 1969) and compare it by means of simulations with MLE and M-estimator.     

On the exact joint distribution of a linear combination of order statistics and their concomitants in an exchangeable multivariate normal distribution

In this work we prove that for an exchangeable multivariate normal distribution the joint distribution of a linear combination of order statistics and a linear combination of their concomitants together with an auxiliary variable is skew normal. We also investigate some special cases, thus extending the results of Olkin and Viana (J Am Stat Assoc 90:1373–1379, 1995), Loperfido (Test 17:370–380, 2008a) and Sheikhi and Jamalizadeh (Paper 52:885–892, 2011).     

Efficiency comparison of unrelated question models based on same privacy protection degree

In this study, the problem of estimating the proportion π _A of people bearing a sensitive attribute A is considered. Three dichotomous unrelated question mechanisms which are alternative to the well-known Simmons’ model are discussed and their performance is evaluated taking into account both efficiency and respondent privacy protection. The variance of the estimators of π _A is compared under equal levels of confidentiality measures introduced by Lanke (1976) and Leysieffer and Warner (1976).     

On diagnostics in multivariate measurement error models under asymmetric heavy-tailed distributions

In this paper, we discuss the extension of some diagnostic procedures to multivariate measurement error models with scale mixtures of skew-normal distributions (Lachos et?al., Statistics 44:541?C556, 2010c). This class provides a useful generalization of normal (and skew-normal) measurement error models since the random term distributions cover symmetric, asymmetric and heavy-tailed distributions, such as skew-t, skew-slash and skew-contaminated normal, among others. Inspired by the EM algorithm proposed by Lachos et?al. (Statistics 44:541?C556, 2010c), we develop a local influence analysis for measurement error models, following Zhu and Lee??s (J R Stat Soc B 63:111?C126, 2001) approach. This is because the observed data log-likelihood function associated with the proposed model is somewhat complex and Cook??s well-known approach can be very difficult to apply to achieve local influence measures. Some useful perturbation schemes are also discussed. In addition, a score test for assessing the homogeneity of the skewness parameter vector is presented. Finally, the methodology is exemplified through a real data set, illustrating the usefulness of the proposed methodology.     

More Powerful Control of the False Discovery Rate Under Dependence

In a breakthrough paper, Benjamini and Hochberg (J Roy Stat Soc Ser B 57:289–300, 1995) proposed a new error measure for multiple testing, the FDR; and developed a distribution-free procedure to control it under independence among the test statistics. In this paper we argue by extensive simulation and theoretical considerations that the assumption of independence is not needed. Along the lines of (Ann Stat 32:1035–1061, 2004b), we moreover provide a more powerful method, that exploits an estimator of the number of false nulls among the tests. We propose a whole family of iterative estimators that prove robust under dependence and independence between the test statistics. These estimators can be used to improve also classical multiple testing procedures, and in general to estimate the weight of a known component in a mixture distribution. Innovations are illustrated by simulations.     

Bayesian parameter inference for partially observed stopped processes

We consider Bayesian parameter inference associated to partially-observed stochastic processes that start from a set B ₀ and are stopped or killed at the first hitting time of a known set A. Such processes occur naturally within the context of a wide variety of applications. The associated posterior distributions are highly complex and posterior parameter inference requires the use of advanced Markov chain Monte Carlo (MCMC) techniques. Our approach uses a recently introduced simulation methodology, particle Markov chain Monte Carlo (PMCMC) (Andrieu et al. 2010), where sequential Monte Carlo (SMC) (Doucet et al. 2001; Liu 2001) approximations are embedded within MCMC. However, when the parameter of interest is fixed, standard SMC algorithms are not always appropriate for many stopped processes. In Chen et al. (2005), Del Moral (2004), the authors introduce SMC approximations of multi-level Feynman-Kac formulae, which can lead to more efficient algorithms. This is achieved by devising a sequence of sets from B ₀ to A and then performing the resampling step only when the samples of the process reach intermediate sets in the sequence. The choice of the intermediate sets is critical to the performance of such a scheme. In this paper, we demonstrate that multi-level SMC algorithms can be used as a proposal in PMCMC. In addition, we introduce a flexible strategy that adapts the sets for different parameter proposals. Our methodology is illustrated on the coalescent model with migration.     

Performance of goodness-of-fit tests for the Cox proportional hazards model with time-varying covariates

There are few readily-implemented tests for goodness-of-fit for the Cox proportional hazards model with time-varying covariates. Through simulations, we assess the power of tests by Cox (J R Stat Soc B (Methodol) 34(2):187–220, 1972), Grambsch and Therneau (Biometrika 81(3):515–526, 1994), and Lin et al. (Biometrics 62:803–812, 2006). Results show that power is highly variable depending on the time to violation of proportional hazards, the magnitude of the change in hazard ratio, and the direction of the change. Because these characteristics are unknown outside of simulation studies, none of the tests examined is expected to have high power in real applications. While all of these tests are theoretically interesting, they appear to be of limited practical value.