A Comparison of Procedures for Controlling the False Discovery Rate in the Presence of Small Variance Genes: A Simulation Study

The Significance Analysis of Microarrays (SAM; Tusher et al., 2001 Tusher , V. G. , Tibshirani , R. , Chu , G. ( 2001 ). Significance analysis of microarrys applied to the ionizing radiation response . Proceedings of the National Academy of Sciences 98 : 5116 – 5121 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) method is widely used in analyzing gene expression data while controlling the FDR by using resampling-based procedure in the microarray setting. One of the main components of the SAM procedure is the adjustment of the test statistic. The introduction of the fudge factor to the test statistic aims at deflating the large value of test statistics due to the small standard error of gene-expression. Lin et al. (2008 Lin , D. , Shkedy , Z. , Burzykowski , T. , Göhlmann , H. W. H. , De Bondt , A. , Perera , T. , Geerts , T. , Bijnens , L. ( 2008 ). Significance analysis of microarray (SAM) for comparisons of several treatments with one control . Biometric Journal, MCP 50 ( 5 ): 801 – 823 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) pointed out that the fudge factor does not effectively improve the power and the control of the FDR as compared to the SAM procedure without the fudge factor in the presence of small variance genes. Motivated by the simulation results presented in Lin et al. (2008 Lin , D. , Shkedy , Z. , Burzykowski , T. , Göhlmann , H. W. H. , De Bondt , A. , Perera , T. , Geerts , T. , Bijnens , L. ( 2008 ). Significance analysis of microarray (SAM) for comparisons of several treatments with one control . Biometric Journal, MCP 50 ( 5 ): 801 – 823 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]), in this article, we extend our study to compare several methods for choosing the fudge factor in the modified t-type test statistics and use simulation studies to investigate the power and the control of the FDR of the considered methods.     

On Estimation of the Bivariate Poisson INAR Process

In a recent article, Pedeli and Karlis (2010 Pedeli, X. and Karlis, D. 2010. A Bivariate INAR(1) Process with Application. Statistical Modelling: An international Journal, 11: 325–349. [Crossref], [Web of Science ®] , [Google Scholar]) examined the extension of the classical Integer–valued Autoregressive (INAR) model to the bivariate case. In the present article, we examine estimation methods for the case of bivariate Poisson innovations. This is a simple extension of the classical INAR model allowing for two discrete valued time series to be correlated. Properties of different estimators are given. We also compare their properties via a small simulation experiment. Extensions to incorporate covariate information is discussed. A real data application is also provided.     

A Generalization of the Skew-Normal Distribution: The Beta Skew-Normal

We consider a new generalization of the skew-normal distribution introduced by Azzalini (1985 Azzalini , A. ( 1985 ). A class of distributions which includes the normal ones . Scand. J. Statis. 12 ( 2 ): 171 – 178 .[Web of Science ®] , [Google Scholar]). We denote this distribution Beta skew-normal (BSN) since it is a special case of the Beta generated distribution (Jones, 2004 Jones , M. C. ( 2004 ). Families of distributions of order statistics . Test 13 ( 1 ): 1 – 43 .[Crossref], [Web of Science ®] , [Google Scholar]). Some properties of the BSN are studied. We pay attention to some generalizations of the skew-normal distribution (Bahrami et al., 2009 Bahrami , W. , Agahi , H. , Rangin , H. ( 2009 ). A two-parameter Balakrishnan skew-normal distribution . J. Statist. Res. Iran 6 : 231 – 242 . [Google Scholar]; Sharafi and Behboodian, 2008 Sharafi , M. , Behboodian , J. ( 2008 ). The Balakrishnan skew-normal density . Statist. Pap. 49 : 769 – 778 .[Crossref], [Web of Science ®] , [Google Scholar]; Yadegari et al., 2008 Yadegari , I. , Gerami , A. , Khaledi , M. J. ( 2008 ). A generalization of the Balakrishnan skew-normal distribution . Statist. Probab. Lett. 78 : 1165 – 1167 .[Crossref], [Web of Science ®] , [Google Scholar]) and to their relations with the BSN.     

Regression M-estimators with One Modified Form of Doubly Censored Data

In this article, we consider the M-estimators for the linear regression model when both response and covariate variables are subject to double censoring. The proposed estimators are constructed as some functional of three types of estimators for a bivariate survival distribution. The first two estimators are the generalizations of the Campbell and Földes (1982 Campbell, G. and Földes, A. 1982. “Large sample properties of nonparametric statistical inference”. In Nonparametric Statistical Inference., Edited by: Gnredenko, B. V., Puri, M. L. and Vineze, I. 103–122. Amsterdam: North-Holland.  [Google Scholar]) and Dabrowska (1988 Dabrowska, D. M. 1988. Kaplan-Meier estimate on the plane. Annals of Statistics, 18: 1475–1489. [Crossref], [Web of Science ®] , [Google Scholar]) estimators proposed by Shen (2009 Shen, P. S. 2009. Nonparametric estimation of the bivariate survival function one modified form of doubly censored data. Computational Statistics, 25: 203–313. [Crossref], [Web of Science ®] , [Google Scholar]). The third estimator is the generalization of the Prentice and Cai (1992 Prentice, R. L. and Cai, J. 1992. Covariance and survivor function estimation using censored multivariate failure time data. Biometrika, 79: 495–512. [Crossref], [Web of Science ®] , [Google Scholar]) estimator. The consistency of the proposed M-estimators is established. A simulation study is conducted to investigate the performance of the proposed estimators. Furthermore, the simple bootstrap methods are used to estimate standard deviations and construct interval estimators.     

A New Generalized Exponential Geometric Distribution

In this article, another version of the generalized exponential geometric distribution different to that of Silva et al. (2010 Silva , R. B. , Barreto-Souza , W. , Cordeiro , G. M. ( 2010 ). A new distribution with decreasing, increasing and upside-down bathtub failure rate. Computat. Statist. Data Anal. 54: 935–944 . [Google Scholar]) is proposed. This new three-parameter lifetime distribution with decreasing, increasing, and bathtub failure rate function is created by compounding the generalized exponential distribution of Gupta and Kundu (1999 Gupta , R. D. , Kundu , D. ( 1999 ). Generalized exponential distributions . Austral. NZ J. Statist. 41 ( 2 ): 173 – 188 .[Crossref], [Web of Science ®] , [Google Scholar]) with a geometric distribution. Some basic distributional properties, moment-generating function, rth moment, and Rényi entropy of the new distribution are studied. The model parameters are estimated by the maximum likelihood method and the asymptotic distribution of estimators is discussed. Finally, an application of the new distribution is illustrated using the two real data sets.     

The Identification of Potential Longitudinal Biomarkers and Measurements of Effectiveness for Biomarkers as Surrogates in Multivariate Survival Data

A proposed method based on frailty models is used to identify longitudinal biomarkers or surrogates for a multivariate survival. This method is an extention of earlier models by Wulfsohn and Tsiatis (1997 Wulfsohn , M. S. , Tsiatis , A. A. ( 1997 ). A joint model for survival and longitudinal data measured with error . Biometrics 53 ( 1 ): 330 – 339 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) and Song et al. (2002 Song , X. , Davidian , M. , Tsiatis , A. A. ( 2002 ). A Semiparametric likelihood approach to joint modeling of longitudinal and time-to-event data . Biometrics 58 ( 4 ): 742 – 753 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]). In this article, similar to Henderson et al. (2002 Henderson , R. , Diggle , P. J. , Dobson , A. ( 2002 ). Identification and efficacy of longitudinal markers for survival . Biostatistics 3 ( 1 ): 33 – 50 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]), a joint likelihood function combines the likelihood functions of the longitudinal biomarkers and the multivariate survival times. We use simulations to explore how the number of individuals, the number of time points per individual and the functional form of the random effects from the longitudianl biomarkers influence the power to detect the association of a longitudinal biomarker and the multivariate survival time. The proposed method is illustrate by using the gastric cancer data.     

On a Generalization of Bivariate Cauchy Distribution

This paper addresses a generalization of the bivariate Cauchy distribution discussed by Fang et al. (1990 Fang , K. T. , Kotz , S. , Ng , K. W. ( 1990 ). Symmetric Multivariate and Related Distributions . London : Chapman and Hall .[Crossref] , [Google Scholar]), derived from a trivariate normal distribution with a general correlation matrix. We obtain explicit expressions for the joint distribution function and joint density function, and show that they reduce in a special case to the corresponding expressions of Fang et al. (1990 Fang , K. T. , Kotz , S. , Ng , K. W. ( 1990 ). Symmetric Multivariate and Related Distributions . London : Chapman and Hall .[Crossref] , [Google Scholar]). Finally, we show that this generalized distribution is useful in determining the orthant probability of a bivariate skew-normal distribution of Azzalini and Dalla Valle (1996 Azzalini , A. , Dalla Valle , A. ( 1996 ). The multivariate skew-normal distribution . Biometrika 83 : 715 – 726 .[Crossref], [Web of Science ®] , [Google Scholar]).     

A Generalization to Bivariate Mittag–Leffler and Bivariate Discrete Mittag–Leffler Autoregressive Processes

A generalization of the Gaver and Lewis (1980 Gaver , D. P. , Lewis , P. A. W. ( 1980 ). First order autoregressive gamma sequences and point processes . Adv. Appl. Probab. 12 : 727 – 745 .[Crossref], [Web of Science ®] , [Google Scholar]) model of first-order autoregressive process with marginals as bivariate Mittag–Leffler distribution is obtained. A necessary and sufficient condition for stationarity of the process is established. Autoregressive process with marginals follow bivariate discrete Mittag–Leffler distribution is also developed. The unknown parameters of the processes are estimated and some numerical results of the estimations are given.     

Improved strategy to collect sensitive data by using geometric distribution as a randomization device

Abstract

In this article, we improvise Singh and Grewal (2013 Singh, S., and I. S. Grewal. 2013. Geometric distribution as a randomization device implemented in the Kuk’s model. International Journal of Contemporary Mathematical Sciences 8:243–8.[Crossref] , [Google Scholar]) and Hussain et al. (2016 Hussain, Z., J. Shabbir, Z. Pervez, S. F. Shah, and M. Khan. 2016. Generalized geometric distribution of order k: A flexible choice to randomize the response. Communications in Statistics: Simulation and Computation 46:4708–21.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) techniques by introducing a new two-stage randomization response process. Using the proposed new technique, we achieve better efficiency and increasing protection of privacy of respondents than the Kuk (1990 Kuk, A. Y. C. 1990. Asking sensitive questions indirectly. Biometrika 77 (2):436–8.[Crossref], [Web of Science ®] , [Google Scholar]), Singh and Grewal (2013 Singh, S., and I. S. Grewal. 2013. Geometric distribution as a randomization device implemented in the Kuk’s model. International Journal of Contemporary Mathematical Sciences 8:243–8.[Crossref] , [Google Scholar]) and Hussain et al. (2016 Hussain, Z., J. Shabbir, Z. Pervez, S. F. Shah, and M. Khan. 2016. Generalized geometric distribution of order k: A flexible choice to randomize the response. Communications in Statistics: Simulation and Computation 46:4708–21.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) models. The relative efficiency and protection of the respondents of the proposed two-stage randomization device have been investigated through simulation study, and the situations are reported where the proposed estimator performs better than its competitors. The SAS code used to investigate the performance of the proposed strategy are also provided.     

On Simultaneous Estimation of the Number of Signals and Frequencies of Multiple Sinusoids When Some Observations Are Missing

In an earlier article (Bai et al., 1999 Bai , Z. D. , Rao , C. R. , Wu , Y. H. , Zen , M. M. , Zhao , L. C. ( 1999 ). The simultaneous estimation of the number of signals and frequencies of multiple sinusods when some observations are missing: I. Asymptotics . Proc. Natl. Acad. Sci. 96 : 11,106 – 11,110 . [CSA] [Crossref], [Web of Science ®] , [Google Scholar]), the problem of simultaneous estimation of the number of signals and frequencies of multiple sinusoids is considered in the case that some observations are missing. The number of signals is estimated with an information theoretic criterion and the frequencies are estimated with eigenvariation linear prediction. Asymptotic properties of the procedure are investigated but the Monte Carlo simulation is not performed. In this article, a slightly different but scale invariant criterion for detection is proposed and the estimation of frequencies remains the same. Asymptotic properties of this new procedure are provided. Monte Carlo Simulation for both procedures is carried out. Furthermore, comparison on the real signals is also given.     

On Complete Convergence for Arrays of Dependent Random Variables

A complete convergence theorem for an array of rowwise independent random variables was established by Sung et al. (2005 Sung , S. H. , Volodin , A. I. , Hu , T.-C. ( 2005 ). More on complete convergence for arrays . Statist. Probab. Lett. 71 : 303 – 311 .[Crossref], [Web of Science ®] , [Google Scholar]). This result has been generalized and extended by Kruglov et al. (2006 Kruglov , V. M. , Volodin , A. I. , Hu , T.-C. ( 2006 ). On complete convergence for arrays . Statist. Probab. Lett. 76 : 1631 – 1640 .[Crossref], [Web of Science ®] , [Google Scholar]) and Chen et al. (2007 Chen , P. , Hu , T.-C. , Liu , X. , Volodin , A. ( 2007 ). On complete convergence for arrays of rowwise negatively associated random variables . Theor. Probab. Appl. 52 : 393 – 397 . [Google Scholar]). In this article, we extend the results of Sung et al. (2005 Sung , S. H. , Volodin , A. I. , Hu , T.-C. ( 2005 ). More on complete convergence for arrays . Statist. Probab. Lett. 71 : 303 – 311 .[Crossref], [Web of Science ®] , [Google Scholar]), Kruglov et al. (2006 Kruglov , V. M. , Volodin , A. I. , Hu , T.-C. ( 2006 ). On complete convergence for arrays . Statist. Probab. Lett. 76 : 1631 – 1640 .[Crossref], [Web of Science ®] , [Google Scholar]), and Chen et al. (2007 Chen , P. , Hu , T.-C. , Liu , X. , Volodin , A. ( 2007 ). On complete convergence for arrays of rowwise negatively associated random variables . Theor. Probab. Appl. 52 : 393 – 397 . [Google Scholar]) to an array of dependent random variables satisfying Hoffmann-Jørgensen type inequalities.     

Estimating Incidence Rate on Current Status Data with Application to a Phase IV Cancer Trial

New drug discovery in the pediatrics has dramatically improved survival, but with long- term adverse events. This motivates the examination of adverse outcomes such as long-term toxicity in a phase IV trial. An ideal approach to monitor long-term toxicity is to systematically follow the survivors, which is generally not feasible. Instead, cross-sectional surveys are conducted in Hudson et al. (2007 Hudson , M. M. , Rai , S. N. , Nunez , C. , Merchant , T. E. , Marina , N. M. , Zalamea , N. , Cox , C. , Phipps , S. , Pompeu , R. , Rosenthal , D. ( 2007 ). Noninvasive evaluation of late anthracycline cardiac toxicity in childhood cancer survivors . J. Clin. Oncol. 25 : 3635 – 3643 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]), with one of the objectives to estimate the cumulative incidence rates along with specific interest in fixed-term (5 or 10 year) rates. We present inference procedures based on current status data to our motivating example with very interesting findings.     

The Alpha-power Tobit Model

The main object of this article is to propose an extension of the tobit model for which the error distribution follows the power-normal distribution (Gupta and Gupta, 2008 Gupta , D. , Gupta , R. C. ( 2008 ). Analyzing skewed data by power normal model . Test 17 : 197 – 210 .[Crossref], [Web of Science ®] , [Google Scholar]). Inference is dealt with by using the likelihood approach. Simulation studies and application to a real data set are used to demonstrate the usefulness of the extension.     

Online Control Charts for Process Averages Based on Repeated Median Filters

Two types of estimates of process level, namely repeated median estimates (Siegel, 1982 Siegel , A. F. ( 1982 ). Robust regression using repeated medians . Biometrika 69 : 242 – 244 .[Crossref], [Web of Science ®] , [Google Scholar]) and full online estimates (Gather et al., 2006 Gather , U. , Schettlinger , K. , Fried , R. ( 2006 ). Online signal extraction by robust linear regression . Computational Statistics 21 : 33 – 51 .[Crossref], [Web of Science ®] , [Google Scholar]) based on repeated median filters, are used to develop control charts. The distributional properties of the estimates are studied using simulation and these are found to closely follow normal distribution. The repeated median being robust against outliers with asymptotically 50% breakdown value and having small standard deviation is found to be useful as a basis for monitoring process averages. The control charts using repeated median estimates have been recommended for general use.     

Tests of Multivariate Independence for Ordinal Data

Population and sample versions of Kendall and Spearman measures of association suitable for multivariate ordinal data are defined. The latter generalize the indices of dependence of Ruymgaart and van Zuijlen (1978 Ruymgaart , F. H. , van Zuijlen , M. C. A. ( 1978 ). Asymptotic normality of multivariate linear rank statistics in the non-i.i.d. case . Ann. Statist. 6 : 588 – 602 .[Crossref], [Web of Science ®] , [Google Scholar]), Joe (1990 Joe , H. ( 1990 ). Multivariate concordance . J. Multivariate Anal. 35 : 12 – 30 .[Crossref], [Web of Science ®] , [Google Scholar]), and Schmid and Schmidt (2007 Schmid , F. , Schmidt , R. ( 2007 ). Multivariate extensions of Spearman's rho and related statistics . Statist. Probab. Lett. 77 : 407 – 416 .[Crossref], [Web of Science ®] , [Google Scholar]) by allowing atoms in the underlying distribution. The representation of the proposed empirical measures as U-statistics enables to establish their asymptotic normality under general distributions. A special attention is given to tests of independence for multivariate ordinal data, where the power of the new methodologies are investigated under fixed and contiguous alternatives.     

Linear Subspace Spanned by Principal Points of a Mixture of Spherically Symmetric Distributions

For each positive integer k, a set of k-principal points of a distribution is the set of k points that optimally represent the distribution in terms of mean squared distance. However, explicit form of k-principal points is often difficult to obtain. Hence a theorem established by Tarpey et al. (1995 Tarpey , T. , Li , L. , Flury , B. D. ( 1995 ). Principal points and self-consistent points of elliptical distributions . Ann. Statist. 23 : 102 – 112 .[Crossref], [Web of Science ®] , [Google Scholar]) has been influential in the literature, which states that when the distribution is elliptically symmetric, any set of k-principal points is in the linear subspace spanned by some principal eigenvectors of the covariance matrix. This theorem is called a “principal subspace theorem”. Recently, Yamamoto and Shinozaki (2000b Yamamoto , W. , Shinozaki , N. ( 2000b ). Two principal points for multivariate location mixtures of spherically symmetric distributions . J. Japan Statist. Soc. 30 : 53 – 63 .[Crossref] , [Google Scholar]) derived a principal subspace theorem for 2-principal points of a location mixture of spherically symmetric distributions. In their article, the ratio of mixture was set to be equal. This article derives a further result by considering a location mixture with unequal mixture ratio.     

DSGE Models with Student-t Errors

This paper deals with Dynamic Stochastic General Equilibrium (DSGE) models under a multivariate student-t distribution for the structural shocks. Based on the solution algorithm of Klein (2000) and the gamma-normal representation of the t-distribution, the TaRB-MH algorithm of Chib and Ramamurthy (2010 Chib , S. , Ramamurthy , S. ( 2010 ). Tailored randomized block MCMC methods with application to DSGE models . Journal of Econometrics 108 : 19 – 38 .[Crossref], [Web of Science ®] , [Google Scholar]) is used to estimate the model. A technique for estimating the marginal likelihood of the DSGE student-t model is also provided. The methodologies are illustrated first with simulated data and then with the DSGE model of Ireland (2004 Ireland , P. N. ( 2004 ). Technology shocks in the new keynesian model . Review of Economics and Statistics 86 ( 4 ): 923 – 936 .[Crossref], [Web of Science ®] , [Google Scholar]) where the results support the t-error model in relation to the Gaussian model.     

Simultaneous Confidence Intervals for the Parameters of Pareto Distribution under Progressive Censoring

In this article, we consider the progressive Type II right censored sample from Pareto distribution. We introduce a new approach for constructing the simultaneous confidence interval of the unknown parameters of this distribution under progressive censoring. A Monte Carlo study is also presented for illustration. It is shown that this confidence region has a smaller area than that introduced by Ku? and Kaya (2007 Ku? , C. , Kaya , M. F. ( 2007 ). Estimation for the parameters of the Pareto distribution under progressive censoring . Commun. Statist. Theor. Meth. 36 : 1359 – 1365 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]).     

The Asymptotic Estimate of Ruin Probability Under a Class of Risk Model in the Presence of Heavy Tails

In contrast with the classical Cramér–Lundberg model where the premium process is a linear function of time, we consider the ruin probability under the risk model where the aggregate premium consists of both a compound Poisson process and a linear process of time. Moreover, a constant interest force is also taken into account in our model. We restrict ourselves to the case where the claim size is heavy-tailed, i.e., the equilibrium distribution function of the claim size belongs to a wide subclass of the subexponential distribution. An asymptotic formula for the ruin probability is obtained by using the similar method of Kalashnikov and Konstantinides (2000 Kalashnikov , V. , Konstantinides , D. ( 2000 ). Ruin under interest force and subexponential claims: a simple treament . Insur. Math. Econ. 27 : 145 – 149 .[Crossref], [Web of Science ®] , [Google Scholar]). The asymptotic formula we get here is the same as the one in Asmussen (1998 Asmussen , S. ( 1998 ). Subexponential asymptotics for stochastic processes: extremal behaviour, stationary distribution and first passage probabilities . Ann. Appl. Probab. 8 : 354 – 374 .[Crossref], [Web of Science ®] , [Google Scholar]), Klüppelberg and Stadtmüller (1998 Klüppelberg , C. , Stadtmüller , U. ( 1998 ). Ruin probabilities in the presence of heavy-tails and interest rates . Scand. Actuarial J. 1 : 49 – 58 .[Taylor & Francis Online] , [Google Scholar]), and Kalashnikov and Konstantinides (2000 Kalashnikov , V. , Konstantinides , D. ( 2000 ). Ruin under interest force and subexponential claims: a simple treament . Insur. Math. Econ. 27 : 145 – 149 .[Crossref], [Web of Science ®] , [Google Scholar]) which did not consider the stochastic premium.     

An Asymmetric Kernel Estimator of Density Function for Stationary Associated Sequences

Here, we apply the smoothing technique proposed by Chaubey et al. (2007 Chaubey , Y. P. , Sen , A. , Sen , P. K. ( 2007 ). A new smooth density estimator for non-negative random variables. Technical Report No. 1/07. Department of Mathematics and Statistics, Concordia University, Montreal, Canada . [Google Scholar]) for the empirical survival function studied in Bagai and Prakasa Rao (1991 Bagai , I. , Prakasa Rao , B. L. S. ( 1991 ). Estimation of the survival function for stationary associated processes . Statist. Probab. Lett. 12 : 385 – 391 .[Crossref], [Web of Science ®] , [Google Scholar]) for a sequence of stationary non-negative associated random variables.The derivative of this estimator in turn is used to propose a nonparametric density estimator. The asymptotic properties of the resulting estimators are studied and contrasted with some other competing estimators. A simulation study is carried out comparing the recent estimator based on the Poisson weights (Chaubey et al., 2011 Chaubey , Y. P. , Dewan , I. , Li , J. ( 2011 ). Smooth estimation of survival and density functions for a stationary associated process using poisson weights . Statist. Probab. Lett. 81 : 267 – 276 .[Crossref], [Web of Science ®] , [Google Scholar]) showing that the two estimators have comparable finite sample global as well as local behavior.