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.     

Population Attributable Fraction as a Measure of Heritability in Dichotomous Twin Data

In many genetic analyses of dichotomous twin data, odds ratios have been used to test hypotheses on heritability and shared common environment effects of a given disease (Lichtenstein et al., 2000 Lichtenstein , P. , Holm , N. , Verkasalo , P. , Iliadou , A. , Kaprio , J. , Koskenvuo , M. , Pukkala , E. , Skytthe , A. , Hemminki , K. ( 2000 ). Environmental and heritable factors in the causation of cancer . New England Journal of Medicine 343 : 78 – 85 .[Crossref], [Web of Science ®] , [Google Scholar]; Ahlbom et al., 1997 Ahlbom , A. , Lichtenstein , P. , Malmström , H. , Feychting , M. , Hemminki , K. , Pedersen , N. L. ( 1997 ). Cancer in twins: genetic and nongenetic familial risk factors . Journal of the National Cancer Institute 89 : 287 – 93 . [Google Scholar]; Ramakrishnan et al., 1992 Ramakrishnan , V. , Goldberg , J. , Henderson , W. , Elsen , S. , True , W. , Lyons , M. , Tsuang , M. ( 1992 ). Elementary methods for the analysis of dichotomous outcomes in unselected samples of twins . Genetic Epidemiology 9 : 273 – 287 . [Google Scholar], 4). However, estimates of these two effects have not been dealt with in the literature. In epidemiology, the attributable fraction (AF), a function of the odds ratio and the prevalence of the risk factor has been used to describe the contribution of a risk factor to a disease in a given population (Leviton, 1973 Leviton , A. ( 1973 ). Definitions of attributable risk . American Journal of Epidemiology 98 : 231 . [Google Scholar]). In this article, we adapt the AF to quantify the heritability and the shared common environment. Twin data on cancer, gallstone disease and phobia are used to illustrate the applicability of the AF estimate as a measure of heritability.     

Comparison of Frailty Models for Acute Leukemia Data under Gompertz Baseline Distribution

In this article, we consider two different shared frailty regression models under the assumption of Gompertz as baseline distribution. Mostly assumption of gamma distribution is considered for frailty distribution. To compare the results with gamma frailty model, we consider the inverse Gaussian shared frailty model also. We compare these two models to a real life bivariate survival data set of acute leukemia remission times (Freireich et al., 1963 Freireich, E.J., Gehan, E., Frei, E., Schroeder, L.R., Wolman, I.J., Anbari, R., Burgert, E.O., Mills, S.D., Pinkel, D., Selawry, O.S., Moon, J.H., Gendel, B.R., Spurr, C.L., Storrs, R., Haurani, F., Hoogstraten, B., Lee, S. (1963). The effect of 6-mercaptopurine on the duration of steroid-induced remissions in acute leukemia: a model for evaluation of other potentially useful therapy. Blood 21:699–716.[Web of Science ®] , [Google Scholar]). Analysis is performed using Markov Chain Monte Carlo methods. Model comparison is made using Bayesian model selection criterion and a well-fitted model is suggested for the acute leukemia data.     

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 Bar-Lev,Bobovitch, and Boukai Randomized Response Models

In this article, two new improved randomized response models have been proposed. The proposed models are found to be more efficient than the recent randomized response model studied by Bar-Lev et al. (2004 Bar-Lev , S. K. , Bobovitch , E. , Boukai , B. ( 2004 ). A note on randomized response models for quantitative data . Metrika 60 : 255 – 260 .[Crossref], [Web of Science ®] , [Google Scholar]). The relative efficiency of the proposed models has been studied with respect to the Bar-Lev et al. (2004 Bar-Lev , S. K. , Bobovitch , E. , Boukai , B. ( 2004 ). A note on randomized response models for quantitative data . Metrika 60 : 255 – 260 .[Crossref], [Web of Science ®] , [Google Scholar]) model under different situations.     

Marginal correlation from an extended random-effects model for repeated and overdispersed counts

Vangeneugden et al. [15 Vangeneugden, T., Molenberghs, G., Laenen, A., Geys, H., Beunckens, C. and Sotto, C. 2007. Marginal correlation in longitudinal binary data based on generalized linear mixed models, Tech. Rep., Hasselt University. submitted for publication [Google Scholar]] derived approximate correlation functions for longitudinal sequences of general data type, Gaussian and non-Gaussian, based on generalized linear mixed-effects models (GLMM). Their focus was on binary sequences, as well as on a combination of binary and Gaussian sequences. Here, we focus on the specific case of repeated count data, important in two respects. First, we employ the model proposed by Molenberghs et al. [13 Molenberghs, G., Verbeke, G. and Demétrio, C. G.B. 2007. An extended random-effects approach to modeling repeated, overdispersed count data. Lifetime Data Anal., 13: 513–531. [Crossref], [PubMed], [Web of Science ®] [Google Scholar]], which generalizes at the same time the Poisson-normal GLMM and the conventional overdispersion models, in particular the negative-binomial model. The model flexibly accommodates data hierarchies, intra-sequence correlation, and overdispersion. Second, means, variances, and joint probabilities can be expressed in closed form, allowing for exact intra-sequence correlation expressions. Next to the general situation, some important special cases such as exchangeable clustered outcomes are considered, producing insightful expressions. The closed-form expressions are contrasted with the generic approximate expressions of Vangeneugden et al. [15 Vangeneugden, T., Molenberghs, G., Laenen, A., Geys, H., Beunckens, C. and Sotto, C. 2007. Marginal correlation in longitudinal binary data based on generalized linear mixed models, Tech. Rep., Hasselt University. submitted for publication [Google Scholar]]. Data from an epileptic-seizures trial are analyzed and correlation functions derived. It is shown that the proposed extension strongly outperforms the classical GLMM.     

A Bottom-Up Dynamic Model of Portfolio Credit Risk with Stochastic Intensities and Random Recoveries

In Bielecki et al. (2014a Bielecki , T. R. , Cousin , A. , Crépey , S. , Herbertsson , A. ( 2014a ). Dynamic hedging of portfolio credit risk in a markov copula model . J. Optimiz. Theor. Applic . doi: DOI 10.1007/s10957-013-0318-4 (forthcoming) .[Crossref] , [Google Scholar]), the authors introduced a Markov copula model of portfolio credit risk where pricing and hedging can be done in a sound theoretical and practical way. Further theoretical backgrounds and practical details are developed in Bielecki et al. (2014b Bielecki , T. R. , Cousin , A. , Crépey , S. , Herbertsson , A. ( 2014b ). A bottom-up dynamic model of portfolio credit risk - Part I: Markov copula perspective . In: Recent Adv. Fin. Eng. 2012 , World Scientific (preprint version available at http://dx.doi.org/10.2139/ssrn.1844574) . [Google Scholar],c) where numerical illustrations assumed deterministic intensities and constant recoveries. In the present paper, we show how to incorporate stochastic default intensities and random recoveries in the bottom-up modeling framework of Bielecki et al. (2014a Bielecki , T. R. , Cousin , A. , Crépey , S. , Herbertsson , A. ( 2014a ). Dynamic hedging of portfolio credit risk in a markov copula model . J. Optimiz. Theor. Applic . doi: DOI 10.1007/s10957-013-0318-4 (forthcoming) .[Crossref] , [Google Scholar]) while preserving numerical tractability. These two features are of primary importance for applications like CVA computations on credit derivatives (Assefa et al., 2011 Assefa , S. , Bielecki , T. R. , Crépey , S. , Jeanblanc , M. ( 2011 ). CVA computation for counterparty risk assessment in credit portfolios . In: Bielecki , T.R. , Brigo , D. , Patras , F. , Eds., Credit Risk Frontiers . Hoboken : Wiley/Bloomberg-Press . [Google Scholar]; Bielecki et al., 2012 Bielecki , T. R. , Crépey , S. , Jeanblanc , M. , Zargari , B. ( 2012 ). Valuation and Hedging of CDS counterparty exposure in a markov copula model . Int. J. Theoret. Appl. Fin. 15 ( 1 ): 1250004 .[Crossref] , [Google Scholar]), as CVA is sensitive to the stochastic nature of credit spreads and random recoveries allow to achieve satisfactory calibration even for “badly behaved” data sets. This article is thus a complement to Bielecki et al. (2014a Bielecki , T. R. , Cousin , A. , Crépey , S. , Herbertsson , A. ( 2014a ). Dynamic hedging of portfolio credit risk in a markov copula model . J. Optimiz. Theor. Applic . doi: DOI 10.1007/s10957-013-0318-4 (forthcoming) .[Crossref] , [Google Scholar]), Bielecki et al. (2014b Bielecki , T. R. , Cousin , A. , Crépey , S. , Herbertsson , A. ( 2014b ). A bottom-up dynamic model of portfolio credit risk - Part I: Markov copula perspective . In: Recent Adv. Fin. Eng. 2012 , World Scientific (preprint version available at http://dx.doi.org/10.2139/ssrn.1844574) . [Google Scholar]) and Bielecki et al. (2014c Bielecki , T. R. , Cousin , A. , Crépey , S. , Herbertsson , A. ( 2014c ). A bottom-up dynamic model of portfolio credit risk - Part II: Common-shock interpretation, calibration and hedging issues . Recent Adv. Fin. Eng. 2012 , World Scientific (preprint version available at http://dx.doi.org/10.2139/ssrn.2245130) . [Google Scholar]).     

Refined Inference on Long Memory in Realized Volatility

There is an emerging consensus in empirical finance that realized volatility series typically display long range dependence with a memory parameter (d) around 0.4 (Andersen et al., 2001 Andersen , T. G. , Bollerslev , T. , Diebold , F. X. , Labys , P. ( 2001 ). The distribution of realized exchange rate volatility . Journal of the American Statistical Association 96 ( 453 ): 42 – 55 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]; Martens et al., 2004 Martnes , M. , Van Dijk , D. , De Pooter , M. ( 2004 ). Modeling and forecasting S&P 500 volatility: Long memory, structural breaks and nonlinearity. Tinbergen Institute Discussion Paper 2004-067/4 . [Google Scholar]). The present article provides some illustrative analysis of how long memory may arise from the accumulative process underlying realized volatility. The article also uses results in Lieberman and Phillips (2004 Lieberman , O. , Phillips , P. C. B. ( 2004 ). Expansions for the distribution of the maximum likelihood estimator of the fractional difference parameter . Econometric Theory 20 ( 3 ): 464 – 484 . [Google Scholar], 2005 Lieberman , O. , Phillips , P. C. B. ( 2005 ). Expansions for approximate maximum likelihood estimators of the fractional difference parameter . The Econometrics Journal 8 : 367 – 379 . [Google Scholar]) to refine statistical inference about d by higher order theory. Standard asymptotic theory has an O(n ^?1/2) error rate for error rejection probabilities, and the theory used here refines the approximation to an error rate of o(n ^?1/2). The new formula is independent of unknown parameters, is simple to calculate and user-friendly. The method is applied to test whether the reported long memory parameter estimates of Andersen et al. (2001 Andersen , T. G. , Bollerslev , T. , Diebold , F. X. , Labys , P. ( 2001 ). The distribution of realized exchange rate volatility . Journal of the American Statistical Association 96 ( 453 ): 42 – 55 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) and Martens et al. (2004 Martnes , M. , Van Dijk , D. , De Pooter , M. ( 2004 ). Modeling and forecasting S&P 500 volatility: Long memory, structural breaks and nonlinearity. Tinbergen Institute Discussion Paper 2004-067/4 . [Google Scholar]) differ significantly from the lower boundary (d = 0.5) of nonstationary long memory, and generally confirms earlier findings.     

On the Feasibility of Basing Horvitz and Thompson's Estimator on a Sample by Rao,Hartley, and Cochran's Scheme

Formulae for the first and second order inclusion probabilities for the Rao et al. (1962 Rao , J. N. K. , Hartley , H. O. , Cochran , W. G. ( 1962 ). On a simple procedure of unequal probability sampling without replacement . J. Roy. Statist. Soc. B 24 : 482 – 491 . [CSA]  [Google Scholar]) (RHC) scheme of sampling are derived. They enable one to evaluate, for a sample drawn according to the RHC scheme, the Horvitz and Thompson's (1952 Horvitz , D. G. , Thompson , D. J. ( 1952 ). A generalization of sampling without replacement from a finite universe . J. Amer. Statist. Assoc. 47 : 663 – 685 . [CSA] [Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) estimator (HTE) along with its unbiased variance estimator given by Yates and Grundy (1953 Yates , F. , Grundy , P. M. ( 1953 ). Selection without replacement from within strata with probability proportional to size . J. Amer. Statist. Assoc. 75 : 206 – 211 . [CSA]  [Google Scholar]). So, for a sample at hand thus drawn one may choose between the RHCE and the HTE for use on finding which one has the smaller coefficient of variation.     

ESTIMATION OF PARAMETERS IN ARFIMA PROCESSES: A SIMULATION STUDY

It is known that, in the presence of short memory components, the estimation of the fractional parameter d in an Autoregressive Fractionally Integrated Moving Average, ARFIMA(p, d, q), process has some difficulties (see [1] Smith, J., Taylor, N. and Yadav, S. 1997. Comparing the bias and misspecification in ARFIMA models. Journal of Time Series Analysis, 18(5): 507–527. [Crossref] , [Google Scholar]). In this paper, we continue the efforts made by Smith et al. [1] Smith, J., Taylor, N. and Yadav, S. 1997. Comparing the bias and misspecification in ARFIMA models. Journal of Time Series Analysis, 18(5): 507–527. [Crossref] , [Google Scholar] and Beveridge and Oickle [2] Beveridge, S. and Oickle, C. 1993. Estimating fractionally integrated time series models. Economics Letters, 43: 137–142.  [Google Scholar] by conducting a simulation study to evaluate the convergence properties of the iterative estimation procedure suggested by Hosking [3] Hosking, J. 1981. Fractional differencing. Biometrika, 68(1): 165–176. [Crossref], [Web of Science ®] , [Google Scholar]. In this context we consider some semiparametric approaches and a parametric method proposed by Fox-Taqqu[4] Fox, R. and Taqqu, M. S. 1986. Large-sample properties of parameter estimates for strongly dependent stationary gaussian time series. The Annals of Statistics, 14(2): 517–532. [Crossref], [Web of Science ®] , [Google Scholar]. We also investigate the method proposed by Robinson [5] Robinson, P. M. 1995a. Log-periodogram regression of time series with long range dependence. The Annals of Statistics, 23(3): 1048–1072. [Crossref], [Web of Science ®] , [Google Scholar] and a modification using the smoothed periodogram function.     

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]).