Detecting a changed segment in DNA sequences

Non-coding deoxyribonucleic acid (DNA) can typically be modelled by a sequence of Bernoulli random variables by coding one base, e.g. T, as 1 and other bases as 0. If a segment of a sequence is functionally important, the probability of a 1 will be different in this changed segment from that in the surrounding DNA. It is important to be able to see whether such a segment occurs in a particular DNA sequence and to pin-point it so that a molecular biologist can investigate its possible function. Here we discuss methods for testing the occurrence of such a changed segment and how to estimate the end points of it. Maximum-likelihood-based methods are not very tractable and so a nonparametric method based on the approach of Pettitt has been developed. The problem and its solution are illustrated by a specific DNA example.     

Designing fractional two-level experiments with nested error structures

A common feature of experiments with a random blocking factor and splitplot experiments is their nested error structure. This paper proposes a general strategy to handle fractional two-level experiments with such error structures. The strategy aims to create error strata with sufficient numbers of contrasts to separate active effects from inactive effects. The strategy also details the construction of treatment generators, given the constraints of a predetermined error structure. The key elements of the strategy are illustrated with a chemical experiment that has 16 factors and 32 runs blocked according to working days, and a cheese-making experiment that has 11 factors and 128 runs, divided over milk supplies as whole plots, curds productions as subplots and sets of identically treated cheeses as sub-subplots.     

On perfect simulation for some mixtures of distributions

This paper studies the implementation of the coupling from the past (CFTP) method of Propp and Wilson (1996) in the set-up of two and three component mixtures with known components and unknown weights. We show that monotonicity structures can be exhibited in both cases, but that CFTP can still be costly for three component mixtures. We conclude with a simulation experiment exhibiting an almost perfect sampling scheme where we only consider a subset of the exhaustive set of starting values.     

Efficacy of programmes for the unemployed: discrete time modelling of duration data from a matched-comparison study

An evaluation is described of two UK Government programmes for the long-term unemployed in Great Britain, Employment Training and Employment Action, using discrete time hazard modelling of event histories. The study design employed a closely matched comparison group and carefully chosen control variables to minimize the effect of selection bias on conclusions. The effect of unobserved heterogeneity is investigated by using some standard random effect model formulations.     

Detecting homogeneous segments in DNA sequences by using hidden Markov models

In recent years there has been a rapid growth in the amount of DNA being sequenced and in its availability through genetic databases. Statistical techniques which identify structure within these sequences can be of considerable assistance to molecular biologists particularly when they incorporate the discrete nature of changes caused by evolutionary processes. This paper focuses on the detection of homogeneous segments within heterogeneous DNA sequences. In particular, we study an intron from the chimpanzee α-fetoprotein gene; this protein plays an important role in the embryonic development of mammals. We present a Bayesian solution to this segmentation problem using a hidden Markov model implemented by Markov chain Monte Carlo methods. We consider the important practical problem of specifying informative prior knowledge about sequences of this type. Two Gibbs sampling algorithms are contrasted and the sensitivity of the analysis to the prior specification is investigated. Model selection and possible ways to overcome the label switching problem are also addressed. Our analysis of intron 7 identifies three distinct homogeneous segment types, two of which occur in more than one region, and one of which is reversible.     

Study of a Markov model for a high-quality dependent process

For high-quality processes, non-conforming items are seldom observed and the traditional p (or np) charts are not suitable for monitoring the state of the process. A type of chart based on the count of cumulative conforming items has recently been introduced and it is especially useful for automatically collected one-at-a-time data. However, in such a case, it is common that the process characteristics become dependent as items produced one after another are inspected. In this paper, we study the problem of process monitoring when the process is of high quality and measurement values possess a certain serial dependence. The problem of assuming independence is examined and a Markov model for this type of process is studied, upon which suitable control procedures can be developed.     

Evaluating the power of Minitab's data subsetting lack of fit test in multiple linear regression

Minitab's data subsetting lack of fit test (denoted XLOF) is a combination of Burn and Ryan's test and Utts' test for testing lack of fit in linear regression models. As an alternative to the classical or pure error lack of fit test, it does not require replicates of predictor variables. However, due to the uncertainty about its performance, XLOF still remains unfamiliar to regression users while the well-known classical lack of fit test is not applicable to regression data without replicates. So far this procedure has not been mentioned in any textbooks and has not been included in any other software packages. This study assesses the performance of XLOF in detecting lack of fit in linear regressions without replicates by comparing the power with the classic test. The power of XLOF is simulated using Minitab macros for variables with several forms of curvature. These comparisons lead to pragmatic suggestions on the use of XLOF. The performance of XLOF was shown to be superior to the classical test based on the results. It should be noted that the replicates required for the classical test made itself unavailable for most of the regression data while XLOF can still be as powerful as the classic test even without replicates.     

Influence diagnostics in the capital asset pricing model under elliptical distributions

In this paper we consider the Capital Asset Pricing Model under Elliptical (symmetric) Distributions. This class of distributions, which contains the normal distribution, t, contaminated normal and power exponential, among others, offers a more flexible framework for modelling asset prices or returns. In order to analyze the sensibility to possible outliers and/or atypical returns of the maximum likelihood estimators, the local influence method was implemented. The results are illustrated by using a set of shares from companies who trade in the Chilean Stock Market. Our main conclusion is that symmetric distributions having heavier tails than those of the normal distribution, especially the t distribution with small degrees of freedom, show a better fit and allow the reduction of the influence of atypical returns in the maximum likelihood estimators.     

Forecasting mortality rates via density ratio modeling

The authors propose a semiparametric approach to modeling and forecasting age‐specific mortality in the United States. Their method is based on an extension of a class of semiparametric models to time series. It combines information from several time series and estimates the predictive distribution conditional on past data. The conditional expectation, which is the most commonly used predictor in practice, is the first moment of this distribution. The authors compare their method to that of Lee and Carter.