Designs for two-colour microarray experiments

Summary.  Designs for two-colour microarray experiments can be viewed as block designs with two treatments per block. Explicit formulae for the A- and D-criteria are given for the case that the number of blocks is equal to the number of treatments. These show that the A- and D-optimality criteria conflict badly if there are 10 or more treatments. A similar analysis shows that designs with one or two extra blocks perform very much better, but again there is a conflict between the two optimality criteria for moderately large numbers of treatments. It is shown that this problem can be avoided by slightly increasing the number of blocks. The two colours that are used in each block effectively turn the block design into a row–column design. There is no need to use a design in which every treatment has each colour equally often: rather, an efficient row–column design should be used. For odd replication, it is recommended that the row–column design should be based on a bipartite graph, and it is proved that the optimal such design corresponds to an optimal block design for half the number of treatments. Efficient row–column designs are given for replications 3–6. It is shown how to adapt them for experiments in which some treatments have replication only 2.     

Robust integer-valued designs for linear random intercept models

This article considers the robust design problem for linear random intercept models with both departures from fixed effects and correlated errors on a finite design space. Two strategies are proposed. One is a worst-case method minimizing the maximum value of the MSE of estimates for the fixed effects over the departure. The other is an average-case method minimizing the average value of the MSE with respect to some priors for the class of departure functions and correlation structures of random errors. Two examples are given to show robust designs for two polynomial models.     

Orthogonal blocking of response surface split-plot designs

When all experimental runs cannot be performed under homogeneous conditions, blocking can be used to increase the power for testing the treatment effects. Orthogonal blocking provides the same estimator of the polynomial effects as the one that would be obtained by ignoring the blocks. In many real-life design scenarios, there is at least one factor that is hard to change, leading to a split-plot structure. This paper shows that for a balanced ordinary least square–generalized least square equivalent split-plot design, orthogonal blocking can be achieved. Orthogonally blocked split-plot central composite designs are constructed and a catalog is provided.     

An algorithm for constructing optimal resolvable incomplete block designs

This paper describes an efficient algorithm for the construction of optimal or near-optimal resolvable incomplete block designs (IBDs) for any number of treatments v < 100. The performance of this algorithm is evaluated against known lattice designs and the 414 or-designs of Patterson & Williams [36]. For the designs under study, it appears that our algorithm is about equally effective as the simulated annealing algorithm of Venables & Eccleston [42]. An example of the use of our algorithm to construct the row (or column) components of resolvable row-column designs is given.     

A simple method for constructing confounded designs for mixed factorial experiments

This paper presents the sinplesr procedure that uses wodular aryithmetic for constructing confounded designs for mixed factorial experiments. The present procedure and the classical one for confounding in symmetrical factorial experiments are both at the same mathema.tical level. The present procedure is written for

practitioners and is lllustrared with several examples.     

Characterization of singular balanced fractional sm factorial designs derivable from balanced arrays with maximum number of constraints

An upper bound on the maximum number of constraints for s-symbol balanced arrays is derived. It is shown that balanced fractional s^m factorial designs derived from some balanced arrays with the maximum possible number of constraints become singular.     

Algorithmic construction of optimal block designs for two-colour cDNA microarray experiments using the linear mixed effects model

ABSTRACT

In this study, methods for efficient construction of A-, MV-, D- and E-optimal or near-optimal block designs for two-colour cDNA microarray experiments with array as the block effect are considered. Two algorithms, namely the array exchange and treatment exchange algorithms together with the complete enumeration technique are introduced. For large numbers of arrays or treatments or both, the complete enumeration method is highly computer intensive. The treatment exchange algorithm computes the optimal or near-optimal designs faster than the array exchange algorithm. The two methods however produce optimal or near-optimal designs with the same efficiency under the four optimality criteria.     

Approximation of IMSE-optimal Designs via Quadrature Rules and Spectral Decomposition

We address the problem of computing integrated mean-squared error (IMSE) optimal designs for interpolation of random fields with known mean and covariance. We assume that the mean squared error is integrated through a discrete measure and restrict the design space to its support. We show that the IMSE and its approximation by spectral truncation can be easily evaluated, which makes their global minimization affordable. Numerical experiments are carried out that illustrate the effectiveness of the approach.     

Adaptive Bayesian compound designs for dose finding studies

We consider the problem of how to efficiently and safely design dose finding studies. Both current and novel utility functions are explored using Bayesian adaptive design methodology for the estimation of a maximum tolerated dose (MTD). In particular, we explore widely adopted approaches such as the continual reassessment method and minimizing the variance of the estimate of an MTD. New utility functions are constructed in the Bayesian framework and are evaluated against current approaches. To reduce computing time, importance sampling is implemented to re-weight posterior samples thus avoiding the need to draw samples using Markov chain Monte Carlo techniques. Further, as such studies are generally first-in-man, the safety of patients is paramount. We therefore explore methods for the incorporation of safety considerations into utility functions to ensure that only safe and well-predicted doses are administered. The amalgamation of Bayesian methodology, adaptive design and compound utility functions is termed adaptive Bayesian compound design (ABCD). The performance of this amalgamation of methodology is investigated via the simulation of dose finding studies. The paper concludes with a discussion of results and extensions that could be included into our approach.     

A review of optimal designs in survey sampling

Results in five areas of survey sampling dealing with the choice of the sampling design are reviewed. In Section 2, the results and discussions surrounding the purposive selection methods suggested by linear regression superpopulation models are reviewed. In Section 3, similar models to those in the previous section are considered; however, random sampling designs are considered and attention is focused on the optimal choice of π_j. Then in Section 4, systematic sampling methods obtained under autocorrelated superpopulation models are reviewed. The next section examines minimax sampling designs. The work in the final section is based solely on the randomization. In Section 6 methods of sample selection which yield inclusion probabilities π_j = n/N and π_ij = n(n - 1)/N(N - 1), but for which there are fewer than _NC_n possible samples, are mentioned briefly.     

Using the chinese remainder theorem in constructing confounded designs for mixed factorial experiments

A procedure for constructing confounded designs for mixed factorial experiments derived from the Chinese Remainder Theorem is presented. The present procedure as well as others, all through use of modular arithmetic, are compared.     

Comparison of rotatable designs for regression on balls,I (quadratic)

Designs for quadratic and cubic regression are considered when the possible choices of the controlable variable are points x=( x₁,x₂,…,x_q) in the q-dimensional. Full of radius R, B_q(R) ={x:Σ⁴_ix²_i?R²}. The designs that are optimum among rotatable designs with respect to the D-, A-, and E-optimality criteria are compared in their performance relative to these and other criteria, including extrapolation. Additionally, the performance of a design optimum for one value of R, when it is implemented for a different value of R, is investigated. Some of the results are developed algebraically; others, numerically. For example, in quadratic regression the A-optimum design appears to be fairly robust in its efficiency, under variation of criterion.     

Randomized response multivariate designs for categorical data

Three approaches to multivariate estimation for categorical data using randomized response (RR) are described. In the first approach, practical only for 2×2 contingency tables, a multi-proportions design is used. In the second approach, a separate RR trial is used for each variate and it is noted that the multi­variate design matrix of conditional probabilities is given by the Kroneeker product of the univariate design matrices of each trial, provided that the trials are independent of each other in a certain sense. The third approach requires only a single randomization and thus may be viewed as the use of vector response. Finally, a special-purpose bivariate design is presented.     

Optimal designs based on exact confidence regions for parameter estimation of a nonlinear regression model

This paper is concerned with the proposal of optimality criteria, referred to as X  - and X^′$X^{\prime }$-optimality criteria, and the construction of X  - and X^′$X^{\prime }$-optimal designs, for nonlinear regression models. These optimal designs aim at improving the estimation of parameters of this class of models. The principle of these criteria is the minimization, with respect to the design, of the expected volume of a particular exact parametric confidence region. In this paper we give detailed definitions, properties, and computation methods of X  - and X^′$X^{\prime }$-optimal designs. We also compare these designs with the classic local D-optimal designs, with regard to robustness and efficiency, for two very well-known academic models (Box–Lucas and Michaelis–Menten models).     

Partially-latinized designs

An interchange optimization algorithm to construct partially-latinized designs is described. The objective function is a weighted linear combination of up to five functions, each of which corresponds to a blocking factor of the required design. Nested simulated annealing is used to address local optima problems. The average efficiency factors of the generated designs are assessed against theoretical upper bounds.     

Screening designs for model discrimination

We introduce new criteria for model discrimination and use these and existing criteria to evaluate standard orthogonal designs. We show that the capability of orthogonal designs for model discrimination is surprisingly varied. In fact, for specified sample sizes, number of factors, and model spaces, many orthogonal designs are not model discriminating by the definition given in this paper, while others in the same class of orthogonal designs are. We also use these criteria to construct optimal two-level model-discriminating designs for screening experiments. The efficacy of these designs is studied, both in terms of estimation efficiency and discrimination success. Simulation studies indicate that the constructed designs result in substantively higher likelihoods of identifying the correct model.     

Optimum mixture designs in some constrained experimental regions

In a mixture experiment, the response depends on the mixing proportions of the components present in the mixture. Optimum designs are available for the estimation of parameters of the models proposed in such situations. However, these designs are found to include the vertex points of the simplex Ξ defining the experimental region, which are not mixtures in the true sense. Recently, Mandal et al. (2015 Mandal, N.K., Pal, M., Sinha, B.K., and Das, P. (2015). Optimum mixture designs in a restricted region. Stat. Pap. 56(1):105–119.[Crossref], [Web of Science ®] , [Google Scholar]) derived optimum designs when the experiment is confined to an ellipsoidal region within Ξ, which does not include the vertices of Ξ. In this paper, an attempt has been made to find optimum designs when the experimental region is a simplex or is cuboidal inside Ξ and does not contain the extreme points.     

Efficient designs for constrained mixture experiments

Many practical experiments on mixtures (where the components sum to one) include additional lower or upper bounds on components, or on linear combinations of them. Usually theory cannot be used to obtain a good design, and algorithmic methods are necessary. Some of the available methods are discussed. Their performance is evaluated on some examples, and the form of the optimal design is investigated.     

Bayes a-opttmal and efficient block designs for comparing test treatments with a standard treatment

A sufficient condition for the Bayes A-optimality of block designs when comparing a standard treatment with v test treatments is given by Majumdar. (In:Optimal Design and Analysis of Experiments, Y. Dodge, V. V. Fedorov and H. P. Wynn (Eds.), 15-27, North-Holland, 1988). The priors that he considers depend on a constant α ε [0, ∞), with α - 0 corresponding to no prior information at all. The given sufficient condition, consequently, also depends on a. Large families of optimal and highly efficient designs are only known for the case α - 0. We will show how some of the results for α - 0 can be extended to obtain large families of optimal and highly efficient designs for arbitrary values of α. In addition, these results are useful when considering design robustness against an improper choice of α.