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.     

Covariate-Adjusted Regression for Time Series

The main purpose of this article is to consider the covariate-adjusted regression (CAR) model for time series. The CAR model was initially proposed by Sentürk and Müller (2005 Sentürk , D. , Müller , H. G. ( 2005 ). Covariate-adjusted regression . Biometrika 92 : 75 – 89 .[Crossref], [Web of Science ®] , [Google Scholar]) for such situations where predictor and response variables are not directly observed, but are distorted by some common observable covariate. Despite CAR being originally designed for independent cross-sectional data, multiple works have extended this method to dependent data setting. In this article, the authors extend CAR to the distorted time series setting. This extension is meaningful in many fields such as econometrics, mathematical finance, and signal processing. The estimates of regression parameters are proposed by establishing connection with functional-coefficient time series model. The consistency and asymptotic normality of the proposed estimates are investigated under the α-mixing conditions. Real data and simulated examples are provided for illustration.     

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.     

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.     

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.     

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.     

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.     

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.     

Bayesian Estimation of Parameters and Comparison of Shared Gamma Frailty Models

In this article, we introduce shared gamma frailty models with three different baseline distributions namely, Weibull, generalized exponential and exponential power distributions. We develop Bayesian estimation procedure using Markov Chain Monte Carlo(MCMC) technique to estimate the parameters involved in these models. We present a simulation study to compare the true values of the parameters with the estimated values. Also we apply these three models to a real life bivariate survival dataset of McGilchrist and Aisbett (1991 McGilchrist, C. A. and Aisbett, C. W. 1991. Regression with frailty in survival analysis. Biometrics, 47: 461–466. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) related to kidney infection data and a better model is suggested for the data.     

Nonnested Testing for Competing Autoregressive Dynamic Models Estimated by Instrumental Variables

In this work we investigate nonnested tests for two competing univariate dynamic linear models with autoregressive disturbances, where the motivation for instrumental variable estimation is mainly due to the recognized presence of current endogenous variables in the regression function, either in one or both models. As the previous transformation of both models yields regression functions which are nonlinear in the parameters, the attractive Gauss-Newton regression (GNR) approach, firstly advocated by Davidson and Mackinnon (1981 Davidson , R. , Mackinnon , J. G. ( 1981 ). Several tests for model specification in the presence of alternative hypotheses . Econometrica 49 : 781 – 93 .[Crossref], [Web of Science ®] , [Google Scholar]), will be used to obtain the results.     

Analyzing Supersaturated Designs by Means of an Information Based Criterion

The cost and time consumption of many industrial experimentations can be reduced using the class of supersaturated designs since this can be used for screening out the important factors from a large set of potentially active variables. A supersaturated design is a design for which there are fewer runs than effects to be estimated. Although there exists a wide study of construction methods for supersaturated designs, their analysis methods are yet in an early research stage. In this article, we propose a method for analyzing data using a correlation-based measure, named as symmetrical uncertainty. This method combines measures from the information theory field and is used as the main idea of variable selection algorithms developed in data mining. In this work, the symmetrical uncertainty is used from another viewpoint in order to determine more directly the important factors. The specific method enables us to use supersaturated designs for analyzing data of generalized linear models for a Bernoulli response. We evaluate our method by using some of the existing supersaturated designs, obtained according to methods proposed by Tang and Wu (1997 Tang , B. , Wu , C. F. J. (1997). A method for constructing supersaturated designs and its E(s ²)-optimality. Canadian Journal of Statistics 25:191–201.[Crossref], [Web of Science ®] , [Google Scholar]) as well as by Koukouvinos et al. (2008 Koukouvinos , C. , Mylona , K. , Simos , D. E. ( 2008 ). E(s ²)-optimal and minimax-optimal cyclic supersaturated designs via multi-objective simulated annealing . Journal of Statistical Planning and Inference 138 : 1639 – 1646 .[Crossref], [Web of Science ®] , [Google Scholar]). The comparison is performed by some simulating experiments and the Type I and Type II error rates are calculated. Additionally, Receiver Operating Characteristics (ROC) curves methodology is applied as an additional statistical tool for performance evaluation.     

Two Statistics for Unconditional Exact Tests in Matched-Pairs Design

Abstract

In a recent article Hsueh et al. (Hsueh, H.-M., Liu, J.-P., Chen, J. J. (2001 Hsueh, H.-M., Liu, J.-P. and Chen, J. J. 2001. Unconditional exact tests for equivalence or noninferiority for paired binary endpoints. Biometrics, 57: 478–483. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar]). Unconditional exact tests for equivalence or noninferiority for paired binary endpoints. Biometrics 57:478–483.) considered unconditional exact tests for paired binary endpoints. They suggested two statistics one of which is based on the restricted maximum-likelihood estimator. Properties of these statistics and the related tests are treated in this article.     

On Joint Determination of the Number of States and the Number of Variables in Markov-Switching Models: A Monte Carlo Study

In this article, we examine the performance of two newly developed procedures that jointly select the number of states and variables in Markov-switching models by means of Monte Carlo simulations. They are Smith et al. (2006 Smith , A. , Naik , P. A. , Tsai , C. ( 2006 ). Markov-switching model selection using Kullback–Leibler divergence . Journal of Econometrics 134 ( 2 ): 553 – 577 .[Crossref], [Web of Science ®] , [Google Scholar]) and Psaradakis and Spagnolo (2006 Psaradakis , Z. , Spagnolo , N. ( 2006 ). Joint determination of the state dimension and autoregressive order for models with Markov regime switching . Journal of Time Series Analysis 27 ( 2 ): 753 – 766 .[Crossref], [Web of Science ®] , [Google Scholar]), respectively. The former develops Markov switching criterion (MSC) designed specifically for Markov-switching models, while the latter recommends the use of standard complexity-penalised information criteria (BIC, HQC, and AIC) in joint determination of the state dimension and the autoregressive order of Markov-switching models. The Monte Carlo evidence shows that BIC outperforms MSC while MSC and HQC are preferable over AIC.     

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.     

Stochastic Comparison on General Inactivity Time and General Residual Life of k-Out-of-n Systems

This paper conducts stochastic comparison on general residual life and general inactivity time of (n ? k + 1)-out-of-n systems and investigates the stochastic behavior of the general inactivity time of a system with units having decreasing reversed hazard rate. These results strengthen some conclusions in both Khaledi and Shaked (2006 Khaledi , B. , Shaked , M. ( 2006 ). Ordering conditional residual lifetimes of coherent systems . Journal of Statistical Planning and Inference 137 : 1173 – 1184 .[Crossref], [Web of Science ®] , [Google Scholar]) and Hu et al. (2007 Hu , T. , Jin , W. , Khaledi , M. ( 2007 ). Ordering conditional distributions of generalized order statistics . Probability in the Engineering and Informational Sciences 21 : 401 – 417 .[Crossref], [Web of Science ®] , [Google Scholar]).     

An Improved Solution for Multiple Comparisons with a Control in Response Surface Methodology with Two Predictor Variables

Sa and Edwards (1993 Sa , P. , Edwards , D. ( 1993 ). Multiple comparisons with a control in response surface methodology . Technometrics 35 ( 4 ): 436 – 445 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) first proposed the Multiple Comparisons with a Control problem in Response Surface Methodology. They provided an exact solution for one predictor variable and a conservative solution when number of predictor variables is more than one. Merchant et al. (1998 Merchant , A. , McCann , M. , Edwards , D. ( 1998 ). Improved multiple comparisons with a control in response surface analysis . Technometrics 40 ( 4 ): 291 – 303 .[Crossref], [Web of Science ®] , [Google Scholar]) improved the solution for the latter case. This article improves Merchant et al.'s solution for the case of rotatable designs in two predictor variables.     

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.     

Relations for Moments of Progressively Type-II Censored Order Statistics from Log-Logistic Distribution with Applications to Inference

In this article, we establish several recurrence relations for the single and product moments of progressively Type-II right censored order statistics from a log-logistic distribution. The use of these relations in a systematic recursive manner would enable the computation of all the means, variances and covariances of progressively Type-II right censored order statistics from the log-logistic distribution for all sample sizes n, effective sample sizes m, and all progressive censoring schemes (R ₁,…, R _m ). The results established here generalize the corresponding results for the usual order statistics due to Balakrishnan and Malik (1987 Balakrishnan , N. , Malik , H. J. ( 1987 ). Moments of order statistics from truncated log-logistic distribution . J. Statist. Plann. Infer. 17 : 251 – 267 .[Crossref], [Web of Science ®] , [Google Scholar]) and Balakrishnan et al. (1987 Balakrishnan , N. , Malik , H. J. , Puthenpura , S. ( 1987 ). Best linear unbiased estimation of location and scale parameters of the log-logistic distribution . Commun. Statist. Theor. Meth. 16 : 3477 – 3495 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]). The moments so determined are then utilized to derive best linear unbiased estimators for the scale- and location-scale log-logistic distributions. A comparison of these estimates with the maximum likelihood estimates is made through Monte Carlo simulation. The best linear unbiased predictors of progressively censored failure times is then discussed briefly. Finally, a numerical example is presented to illustrate all the methods of inference developed here.     

Bias-Corrected Maximum Likelihood Estimators in Nonlinear Heteroscedastic Models

Nonlinear heteroscedastic models are widely used in econometrics and statistical applications. We derive matrix formulae for the second-order biases of the maximum likelihood estimators of the parameters in the mean and variance response which generalize previous results by Cook et al. (1986 Cook , D. R. , Tsai , C. L. , Wei , B. C. ( 1986 ). Bias in nonlinear regression . Biometrika 73 : 615 – 623 .[Crossref], [Web of Science ®] , [Google Scholar]) and Cordeiro (1993 Cordeiro , G. M. ( 1993 ). Bartlett corrections and bias correction for two heteroscedastic regression models . Commun. Statist. Theor. Meth. 22 : 169 – 188 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]). The biases of the estimators are easily obtained as vectors of regression coefficients from suitable weighted linear regressions. The practical use of such biases is illustrated in a simulation study and in an application to a real data set.     

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.