Case–control genome-wide joint association study using semiparametric empirical model and approximate Bayes factor

We propose a semiparametric approach for the analysis of case–control genome-wide association study. Parametric components are used to model both the conditional distribution of the case status given the covariates and the distribution of genotype counts, whereas the distribution of the covariates are modelled nonparametrically. This yields a direct and joint modelling of the case status, covariates and genotype counts, and gives a better understanding of the disease mechanism and results in more reliable conclusions. Side information, such as the disease prevalence, can be conveniently incorporated into the model by an empirical likelihood approach and leads to more efficient estimates and a powerful test in the detection of disease-associated SNPs. Profiling is used to eliminate a nuisance nonparametric component, and the resulting profile empirical likelihood estimates are shown to be consistent and asymptotically normal. For the hypothesis test on disease association, we apply the approximate Bayes factor (ABF) which is computationally simple and most desirable in genome-wide association studies where hundreds of thousands to a million genetic markers are tested. We treat the approximate Bayes factor as a hybrid Bayes factor which replaces the full data by the maximum likelihood estimates of the parameters of interest in the full model and derive it under a general setting. The deviation from Hardy–Weinberg Equilibrium (HWE) is also taken into account and the ABF for HWE using cases is shown to provide evidence of association between a disease and a genetic marker. Simulation studies and an application are further provided to illustrate the utility of the proposed methodology.     

Cointegration Detection Using Dynamic Factor Models

A method of information-criterion-based cointegration detection using dynamic factor models is proposed. The results of the data-based and non data-based Monte Carlo simulations suggest that this method is as effective as conventional hypothesis-testing methods. In the proposed method, an observed multivariate time series is described in terms of common stochastic trends plus stationary autoregressive cycles. Then the best model is selected from among alternative models obtained by changing the number of common stochastic trends, on the basis of information criteria. Consequently, the cointegration rank is determined on the basis of the selected model. Two advantages of the proposed method are also discussed.     

Computational algorithms for the factor model

Algorithms for computing the maximum likelihood estimators and the estimated covariance matrix of the estimators of the factor model are derived. The algorithms are particularly suitable for large matrices and for samples that give zero estimates of some error variances. A method of constructing estimators for reduced models is presented. The algorithms can also be used for the multivariate errors-in-variables model with known error covariance matrix.     

Practical bayesian approaches to the analystcs of a 2×2 contingency table with incompletely categorized data

To assess the efficacy of a treatment, patients are administered a pre-test, the treatment, and a post-test (identical to the pre-test). These patients are then categorized according to their outcomes observed on both tests,e.g., (S,S), (S,F), etc. Also, we observe "incomplete" information on the pre-tests' outcomes for some patients and the results of only the post-test being known for thers, A Bayesian framework is fit to the problem and Bayes factors, posterior odds ratios, and utility functions are given to evaluate th e treatment, A method of assessing the prior distribution is specified and a numerical example is worked.     

A comparison of random balance and two-stage group screening designs: A case study

In this paper we focus on the problem of supersaturated (fewer runs than factors) screening experiments. We consider two major types of designs which have been proposed in this situ¬ation: random balance and two-stage group screening. We discuss the relative merits and demerits of each strategy. In addition, we compare the performance of these strategies by means of a case study in which 100 factors are screened in 20,42,62, and 84 runs.     

Quadratic perturbation expansions of certain functions of eigenvalues and eigenvectors and their application to sensitivity analysis in multivariate methods

Tanaka (1988) lias derived the influence functions, which are equivalent to the perturbation expansions up to linear terms, of two functions of eigenvalues and eigenvectors of a real symmetric matrix, and applied them to principal component analysis. The present paper deals with the perturbation expansions up to quadratic terms of the same functions and discusses their application to sensitivity analysis in multivariate methods, in particular, principal component analysis and principal factor analysis. Numerical examples are given to show how the approximation improves with the quadratic terms.     

Influence in covariance structure analysis: with an application to confirmatory factor analysis

Influence functions are derived for the parameters in covariance structure analysis, where the parameters are estimated by minimizing a discrepancy function between the assumed covariance matrix and the sample covariance matrix. The case of confirmatory factor analysis is studied precisely with a numerical example. Comparing with a general procedure called one-step estimation, the proposed procedure has two advantages:1) computing cost is cheaper, 2) the property that arbitrary influence can be decomposed into a fi-nite number of components discussed by Tanaka and Castano-Tostado(1990) can be used for efficient computing and the characterization of a covariance structure model from the sensitivity perspective. A numerical comparison is made among the confirmatory factor analysis and some procedures of ex-ploratory factor analysis by using the decomposition mentioned above.     

Bayesian Approaches to Nonparametric Estimation of Densities on the Unit Interval

This paper investigates nonparametric estimation of density on [0, 1]. The kernel estimator of density on [0, 1] has been found to be sensitive to both bandwidth and kernel. This paper proposes a unified Bayesian framework for choosing both the bandwidth and kernel function. In a simulation study, the Bayesian bandwidth estimator performed better than others, and kernel estimators were sensitive to the choice of the kernel and the shapes of the population densities on [0, 1]. The simulation and empirical results demonstrate that the methods proposed in this paper can improve the way the probability densities on [0, 1] are presently estimated.     

BIVARIATE DISTRIBUTION WITH TRUNCATED POISSON MARGINAL DISTRIBUTIONS

ABSTRACT

A bivariate distribution, whose marginal distributions are truncated Poisson distributions, is developed as a product of truncated Poisson distributions and a multiplicative factor. The multiplicative factor takes into account the correlation, either positive or negative, between the two random variables. The distributional properties of this model are studied and the model is fitted to a real life bivariate data.