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Time-dependent receiver operating characteristic (ROC) curves and their area under the curve (AUC) are important measures to evaluate the prediction accuracy of biomarkers for time-to-event endpoints (e.g., time to disease progression or death). In this article, we propose a direct method to estimate AUC(t) as a function of time t using a flexible fractional polynomials model, without the middle step of modeling the time-dependent ROC. We develop a pseudo partial-likelihood procedure for parameter estimation and provide a test procedure to compare the predictive performance between biomarkers. We establish the asymptotic properties of the proposed estimator and test statistics. A major advantage of the proposed method is its ease to make inference and to compare the prediction accuracy across biomarkers, rendering our method particularly appealing for studies that require comparing and screening a large number of candidate biomarkers. We evaluate the finite-sample performance of the proposed method through simulation studies and illustrate our method in an application to AIDS Clinical Trials Group 175 data.

Case–parent trio studies concerned with children affected by a disease and their parents aim to detect single nucleotide polymorphisms (SNPs) showing a preferential transmission of alleles from the parents to their affected offspring. A popular statistical test for detecting such SNPs associated with disease in this study design is the genotypic transmission/disequilibrium test (gTDT) based on a conditional logistic regression model, which usually needs to be fitted by an iterative procedure. In this article, we derive exact closed-form solutions for the parameter estimates of the conditional logistic regression models when testing for an additive, a dominant, or a recessive effect of a SNP, and show that such analytic parameter estimates also exist when considering gene–environment interactions with binary environmental variables. Because the genetic model underlying the association between a SNP and a disease is typically unknown, it might further be beneficial to use the maximum over the gTDT statistics for the possible effects of a SNP as test statistic. We therefore propose a procedure enabling a fast computation of the test statistic and the permutation-based p-value of this MAX gTDT. All these methods are applied to whole-genome scans of the case–parent trios from the International Cleft Consortium. These applications show our procedures dramatically reduce the required computing time compared to the conventional iterative methods allowing, for example, the analysis of hundreds of thousands of SNPs in a few minutes instead of several hours.

Summary Of interest is the analysis of results of a series of experiments repeated at several environments with the same set of plant varieties. Suppose that the experiments, multi-environment variety trials, are all conducted in resolvable incomplete block (IB) designs. Following the randomization approach adopted in Calinski and Kageyama (2000, Lecture Notes in Statistics, 150), two models for analyzing such trial data can be considered. One is derived under a complete additivity assumption, the other takes into account possible different responses of the varieties to variable environmental conditions. The analysis under the first, the standard model, does not provide answers to questions related to the performance of the individual varieties at different environments. These can be considered when using the more general second model. The purpose of this article is to devise interesting parameter estimation and hypothesis testing procedures under that more realistic model. Its application is illustrated by a thorough analysis of a set of data from a winter wheat series of trials.

Cancerous tumor growth creates cells with abnormal DNA. Allelic-loss experiments identify genomic deletions in cancer cells, but sources of variation and intrinsic dependencies complicate inference about the location and effect of suppressor genes; such genes are the target of these experiments and are thought to be involved in tumor development. We investigate properties of an instability-selection model of allelic-loss data, including likelihood-based parameter estimation and hypothesis testing. By considering a special complete-data case, we derive an approximate calibration method for hypothesis tests of sporadic deletion. Parametric bootstrap and Bayesian computations are also developed. Data from three allelic-loss studies are reanalyzed to illustrate the methods.

SUMMARY After a brief review of commonly used methods for parameter estimation from ligand-binding data in the biochemistry literature, we propose some diagnostic checks and statistical tests of the underlying assumptions and develop methods for evaluating the biases and variances of the estimates and for constructing confidence intervals. Examples on the analysis of data from two radioligand-binding experiments are presented to illustrate these methods.

A model specified in terms of linear models for marginal logits and linear models for log-odds ratios is proposed for the analysis of two-period binary cross-over experiments. Hypothesis testing and parameter estimation are facilitated by standard likelihood methodology. Two examples are used to illustrate how the model can be used to analyze two-period binary cross-over experiments. Results from a simulation study demonstrate that this approach to the analysis of binary cross-over data compares favorably with standard procedures, such as the Mainland-Gart test for a treatment difference, Prescott's test for a treatment difference, and the Hills-Armitage test for treatment-by-period interaction.

We consider the problem of studying several dose combinations of two drugs for a therapeutic endpoint in a multilevel factorial clinical trial. Two test statistics are constructed to test whether there exists at least one dose combination that is more effective than its component doses. Their distributions involve nuisance parameters quantifying the mean differences among the doses of the two component drugs. It is shown that their power functions achieve maxima as all the nuisance parameters approach infinity in absolute value. The significance levels of the two tests are derived and two alpha-level tests are proposed. Tables are given to provide the alpha-level critical values for these tests and to gain insights into their power performances.

For many measurements made on processes and individuals, the true value being measured is unknown or unknowable. When data consist of two or more distinct methods of measurement, the problem of comparing measurements is often referred to as comparative calibration. A provisional analysis of such data can be made assuming one method or set of measurements is unbiased, by means of the classic functional relationship model. Assuming normality in the multivariate case (i.e., more than two methods of measurement), maximum likelihood estimates are usually calculated using generalized eigenvalues and eigenvectors. We propose calculating the same maximum likelihood estimates using a simple EM algorithm. The problems of estimating the variance of parameter estimates and testing the hypothesis of equal calibration lines are considered. An alternative error assumption for the basic model is also explored. The proposed methods are validated using simulation.