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.     

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.     

Empirical Likelihood Method for Censored Median Regression Models

Based on the semiparametric median regression analysis for the right-censored data developed by Ying et al. (1995 Ying , Z. , Jung , S. H. , Wei , L. J. ( 1995 ). Survival analysis with median regression models . J. Amer. Statist. Assoc. 90 : 178 – 184 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]), an empirical likelihood based inferential procedure for the regression coefficients is proposed. The limiting distribution of the proposed log-empirical likelihood ratio test statistic follows a chi-squared distribution, which corresponds to the standard asymptotic results of the empirical likelihood method. The inference about the subsets of the entire regression coefficients vector is discussed. The proposed method is illustrated by some simulation studies.     

General Saddlepoint Approximations: Application to the Anderson-Darling Test Statistic

We consider the relative merits of various saddlepoint approximations for the cumulative distribution function (cdf) of a statistic with a possibly non normal limit distribution. In addition to the usual Lugannani-Rice approximation, we also consider approximations based on higher-order expansions, including the case where the base distribution for the approximation is taken to be non normal. This extends earlier work by Wood et al. (1993 Wood , A. T. A. , Booth , J. G. , Butler , R. W. ( 1993 ). Saddlepoint approximations to the CDF of some statistics with nonnormal limit distributions . Journal of the American Statistical Association 88 : 680 – 686 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]). These approximations are applied to the distribution of the Anderson-Darling test statistic. While these generalizations perform well in the middle of the distribution's support, a conventional normal-based Lugannani-Rice approximation (Giles, 2001 Giles , D. E. A. ( 2001 ). A Saddlepoint approximation to the distribution function of the Anderson-Darling test statistic . Communications in Statistics B 30 : 899 – 905 .[Taylor & Francis Online] , [Google Scholar]) is superior for conventional critical regions.     

Semiparametric Efficient Distribution Free Estimation of Panel Models

This article generalizes results from Park et al. (1998 Park , B. U. , Sickles , R. C. , Simar , L. ( 1998 ). Stochastic frontiers: a semiparametric approach . J. Econometrics 84 : 273 – 301 .[Crossref], [Web of Science ®] , [Google Scholar]) and Adams et al. (1999 Adams , R. M. , Berger , A. N. , Sickles , R. C. ( 1999 ). Semiparametric approaches to stochastic panel frontiers with applications in the banking industry . J. Bus. Econ. Statist. 17 : 349 – 358 .[Taylor & Francis Online] , [Google Scholar]) on semiparametric efficient estimation of panel models. The form of semiparametric efficient estimators depends on the statistical assumptions imposed. Normality assumptions on the transitory error are sometimes inappropriate. We relax the normality assumption used in the articles above to derive more general semiparametric efficient estimators. These estimators are illustrated in a Monte Carlo simulation and an analysis of banking productivity.     

Quantile-based Chernoff distance for truncated random variables

Several probability distributions such as power-Pareto distribution (see Gilchrist 2000 Gilchrist, W. 2000. Statistical modelling with quantile functions. Boca Raton, FL: Chapman and Hall/CRC.[Crossref] , [Google Scholar] and Hankin and Lee 2006 Hankin, R. K. S., and A. Lee. 2006. A new family of non-negative distributions. Australian and New Zealand Journal of Statistics 48:67–78.[Crossref], [Web of Science ®] , [Google Scholar]), various forms of lambda distributions (see Ramberg and Schmeiser 1974 Ramberg, J. S., and B. W. Schmeiser. 1974. An appropriate method for generating asymmetric random variables. Communications of the ACM 17:78–82.[Crossref], [Web of Science ®] , [Google Scholar] and Freimer et al. 1988 Freimer, M., S. Mudholkar, G. Kollia, and C. T. Lin. 1988. A study of the generalized lambda family. Communications in Statistics - Theory and Methods 17:3547–67.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]), Govindarajulu distribution (see Nair, Sankaran, and Vineshkumar 2012 Nair, U. N., P. G. Sankaran, and B. Vineshkumar. 2012. The Govindarajulu distribution: some properties and applications. Communications in Statistics—Theory and Methods 41:4391–406.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]), etc., do not have manageable distribution functions, though they have tractable quantile functions. Hence, analytical study of the properties of Chernoff distance of two random variables associated with these distributions via traditional distribution function-based tool becomes difficult. To make this simple, in this paper, we introduce quantile-based Chernoff distance for (left or right) truncated random variables and study its various properties. Some useful bounds as well as characterization results are obtained.     

Methods for Bivariate Survival Data with Mismeasured Covariates Under an Accelerated Failure Time Model

Accelerated failure time models are useful in survival data analysis, but such models have received little attention in the context of measurement error. In this paper we discuss an accelerated failure time model for bivariate survival data with covariates subject to measurement error. In particular, methods based on the marginal and joint models are considered. Consistency and efficiency of the resultant estimators are investigated. Simulation studies are carried out to evaluate the performance of the estimators as well as the impact of ignoring the measurement error of covariates. As an illustration we apply the proposed methods to analyze a data set arising from the Busselton Health Study (Knuiman et al., 1994 Knuiman , M. W. , Cullent , K. J. , Bulsara , M. K. , Welborn , T. A. , Hobbs , M. S. T. ( 1994 ). Mortality trends, 1965 to 1989, in Busselton, the site of repeated health surveys and interventions . Austral. J. Public Health 18 : 129 – 135 . [CSA] [Crossref], [PubMed] , [Google Scholar]).     

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.     

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.     

On simulation of normal records

ABSTRACT

In the present paper, we discuss algorithms of record generation when records are taken from a normal population. We propose three new generation algorithms, compare their efficiency and find the most efficient algorithm (Algorithm 2.1). We then compare these algorithms with known generation algorithms presented in the work of Balakrishnan, So, and Zhu (2016 Balakrishnan, N., H. Y. So, and X. J. Zhu. 2016. On Box-Muller transformation and simulation of normal record data. Communication in Statistics – Simulation and Computations 45(10):3670–82.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]).     

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.     

Improved Predictive Inference for Responses Based on Location Parameter Median from the Rayleigh Model Given a Doubly Censored Sample

The purpose of this article is to investigate the predictive inference for responses from the location parameter mean as well as from the median given a doubly censored sample from the two-parameter Rayleigh model. The predictive results by Khan et al. (2010 Khan , H. M. R. , Provost , S. B. , Ashima , S. ( 2010 ). Predictive Inference from a Two-Parameter Rayleigh Life Model Given a Doubly Censored Sample . Commun. Statist. Theor. Meth. 39 ( 7 ): 1237 – 1246 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) are used to obtain the predictive inference for responses from the median, where Khan et al. (2010 Khan , H. M. R. , Provost , S. B. , Ashima , S. ( 2010 ). Predictive Inference from a Two-Parameter Rayleigh Life Model Given a Doubly Censored Sample . Commun. Statist. Theor. Meth. 39 ( 7 ): 1237 – 1246 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) obtained the future estimates from the mean. A numerical example representing 66 liver cancer patients is used for predictive analysis. It is concluded that the predictive inference from the median gives precise results as compared with the location parameter mean.     

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.     

A Class of Two-Sample Nonparametric Tests for Panel Count Data

Panel count data frequently occur in many situations including medical follow-up studies and reliability experiments. For two-sample comparison based on panel count data, several procedures have been proposed including Thall and Lachin (1988 Thall , P. F. , Lachin , J. M. ( 1988 ). Analysis of recurrent events: nonparametric methods for random-interval count data . J. Amer. Statist. Assoc. 83 : 339 – 347 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) and Sun and Fang (2003 Sun , J. , Fang , H. B. ( 2003 ). A nonparametric test for panel count data . Biometrika 90 : 199 – 208 .[Crossref], [Web of Science ®] , [Google Scholar]). In this article, a new class of nonparametric test procedures are presented. The test is a generalization of that for the same problem for failure time data and overcomes some shortcomings of the existing methods. Monte Carlo simulation studies are conducted to evaluate the presented approach and suggest that it works well. An illustrative example is discussed.     

D s -Optimal Designs for Quadratic Log Contrast Model for Experiments with Mixtures

The approximate D _s -optimal design for discriminating between linear and quadratic log contrast models for experiments with mixtures suggested by Aitchison and Bacon-Shone (1984 Aitchison , J. , Bacon-Shone , J. ( 1984 ). Log contrast models for experiments with mixtures . Biometrika 71 : 323 – 330 .[Crossref], [Web of Science ®] , [Google Scholar]) is investigated, where the experimental domain is restricted further as in Chan (1992 Chan , L. Y. ( 1992 ). D-Optimal design for a quadratic log contrast model for experiments with mixtures . Commun. Statist. Theor. Meth. 21 ( 10 ): 2909 – 2930 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]). It is found that for a symmetric subspace of the finite dimensional simplex, there is a D _s -optimal design with the nice structure that puts a weight 1/2 ^k?1 on the centroid of this subspace and the remaining weight is uniformly distributed on the vertices of the experimental domain. Finally, the D _s -efficiency of the D-optimal design for quadratic model and the design given by Aitchison and Bacon-Shone (1984 Aitchison , J. , Bacon-Shone , J. ( 1984 ). Log contrast models for experiments with mixtures . Biometrika 71 : 323 – 330 .[Crossref], [Web of Science ®] , [Google Scholar]) are also discussed.     

Saddlepoint Approximations to the Limiting Distribution of the Modified Anderson–Darling Test Statistic

The approximation for the distribution function of test statistic is extremely important in statistics. The standard and higher-order saddlepoint approximations are considered in tails of the limiting distribution for the modified Anderson–Darling test. The saddlepoint approximations are compared with the approximation of Sinclair et al. (1990 Sinclair , C. D. , Spurr , B. D. , Ahmad , M. I. ( 1990 ). Modified Anderson Darling test . Communication Statistics—Theory and Methods 19 : 3677 – 3686 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) for upper tail area. An empirical function is derived to estimate the critical values of a saddlepoint approximation.     

The flexible skew Laplace distribution

ABSTRACT

Skew-symmetric distributions have been discussed by several research-ers. In this article we construct a skew-symmetric Laplace distribution, which is the generalization of distribution given by Ali et al. (2009 Ali, M., Pal, M., Woo, J. (2009). Skewed reflected distributions generated by the Laplace kernel. Aust. J. Statist. 38:45–58. [Google Scholar]) and Nekoukhou and Alamatsaz (2012 Nekoukhou, V., Alamatsaz, M.H. (2012). A family of skew-symmetric-Laplace distributions. Statist. Papers. 53(3):685–696.[Crossref], [Web of Science ®] , [Google Scholar]). This new distribution contains more parameters, and this induces flexibility properties, such as unimodality or bimodality. We study on some properties of this distribution. In the last section we also provide an application with a real data. Concerning example has recently been discussed by Nekoukhou et al. (2013 Nekoukhou, V., Alamatsaz, M.H., Aghajani, A.H. (2013). A flexible skew-generalized normal distribution. Commun. Statist. Theory Methods. 42(13):2324–2334.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) to apply to their model. We compare the behavior of our distribution to their distribution on this example.     

The Finite Time Ruin Probability of a New Risk Model Based on Entrance Process

In this article, we consider a new insurance risk model based on the entrance process proposed in Li et al. (2005 Li , Z. , Zhu , J. , Chen , F. ( 2005 ). Study of a risk model based on the entrance process . Statist. Probab. Lett. 72 : 1 – 10 .[Crossref], [Web of Science ®] , [Google Scholar]), and investigate the finite time ruin probabilities of this model. It is showed that an exponential upper bound for the finite time ruin probability exists, when the distributions of the claim size are light tailed. Furthermore, when the distributions of the claim size are heavy tailed, an asymptotic formula for the finite time ruin probability is obtained.     

Bias Correction in Generalized Nonlinear Models with Dispersion Covariates

We derive general formulae for the second-order biases of maximum likelihood estimates of the parameters in generalized nonlinear models with dispersion covariates. This result generalizes previous work by Botter and Cordeiro (1998 Botter , D. A. , Cordeiro , G. M. ( 1998 ). Improved estimates for generalized linear models with dispersion covariates . J. Statist. Comput. Simul. 62 : 91 – 104 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) and Cordeiro and McCullagh (1991 Cordeiro , G. M. , McCullagh , P. ( 1991 ). Bias correction in generalized linear models . J. Roy Statist. Soc. B 53 : 629 – 643 . [Google Scholar]). The practical use of such bias corrections is illustrated in a simulation study.