Balanced Factorial Designs for cDNA Microarray Experiments

Balanced factorial designs are introduced for cDNA microarray experiments. Single replicate designs obtained using the classical method of confounding are shown to be particularly useful for deriving suitable balanced designs for cDNA microarrays. Classical factorial designs obtained using methods other than the method of confounding are also shown to be useful. The paper provides a systematic method of deriving designs for microarray experiments as opposed to algorithmic and ad-hoc methods and generalizes several of the microarray designs given recently in the literature.     

Some methods for constructing efficiency-balanced block designs

Three methods are presented for constructing connected efficiency-balanced block designs from other block designs with the same properties. The resulting designs differ from the original ones in the number of blocks and/or in the number of experimental units and their arrangement, while the number of treatments remains unaltered. Some remarks on the proposed methods of construction refer also to variance-balanced block designs.     

Response surface design evaluation and comparison

Designing an experiment to fit a response surface model typically involves selecting among several candidate designs. There are often many competing criteria that could be considered in selecting the design, and practitioners are typically forced to make trade-offs between these objectives when choosing the final design. Traditional alphabetic optimality criteria are often used in evaluating and comparing competing designs. These optimality criteria are single-number summaries for quality properties of the design such as the precision with which the model parameters are estimated or the uncertainty associated with prediction. Other important considerations include the robustness of the design to model misspecification and potential problems arising from spurious or missing data. Several qualitative and quantitative properties of good response surface designs are discussed, and some of their important trade-offs are considered. Graphical methods for evaluating design performance for several important response surface problems are discussed and we show how these techniques can be used to compare competing designs. These graphical methods are generally superior to the simplistic summaries of alphabetic optimality criteria. Several special cases are considered, including robust parameter designs, split-plot designs, mixture experiment designs, and designs for generalized linear models.     

The effect of small sample on optimal designs for logistic regression models

Asymptotic methods are commonly used in statistical inference for unknown parameters in binary data models. These methods are based on large sample theory, a condition which may be in conflict with small sample size and hence leads to poor results in the optimal designs theory. In this paper, we apply the second order expansions of the maximum likelihood estimator and derive a matrix formula for the mean square error (MSE) to obtain more precise optimal designs based on the MSE. Numerical results indicate the new optimal designs are more efficient than the optimal designs based on the information matrix.     

Designs for cropping systems research

The present article establishes equivalence between extended group divisible (EGD) designs and designs for crop sequence experiments. This equivalence has encouraged the agricultural experimenters to use EGD designs for their experimentation. Some real life applications of EGD designs have been given. It has also been shown that several existing association schemes are special cases of EGD association scheme. Some methods of construction of EGD designs are also given. A catalogue of EGD designs obtainable through methods of construction along with efficiency factors of various factorial effects is also presented. In some crop sequence experiments that are conducted to develop suitable integrated nutrient supply system of a crop sequence, the treatments do not comprise of a complete factorial structure. The experimenter is interested in estimating the residual and direct effect of the treatments along with their cumulative effects. For such experimental settings block designs with two sets of treatments applied in succession are the appropriate designs. The correspondence established between row–column designs and block designs for two stage experiments by Parsad et al. [2003. Structurally incomplete row–column designs. Comm. Statist. Theory Methods 32(1), 239–261] has been exploited in obtaining designs for such experimental situations. Some open problems related to designing of crop sequence experiments are also given.     

Adaptative Designs for Multi-Arm Clinical Trials: The Play-the-Winner Rule Revisited

Adaptative designs for clinical trials that are based on a generalization of the “play-the-winner” rule are considered as an alternative to previously developed models. Theoretical and numerical results show that these designs perform better for the usual criteria. Bayesian methods are proposed for the statistical analysis of these designs.     

Some families of group divisible designs

Generalizing methods of constructions of Hadamard group divisible designs due to Bush (1979), some new families of semi-regular or regular group divisible designs are produced. Furthermore, new nonisomorphic solutions for some known group divisible designs are given, together with useful group divisible designs not listed in Clatworthy (1973).     

Families of neighbour designs and their analysis

Several methods of construction of generalised neighbour designs of equal and unequal block sizes are presented alongwith examples. Some methods for constructing neighbour designs of Rees are also given. The outline of analysis of generalised neighbour design has also been suggested.     

Optimal repeated measurements designs for comparing test treatments with a control

A-optimal and mv optimal repeated measurments designs for comparing serveral test treatments with a control are considered. the models considered are basically of two types: without preperides and the cirular model. It is shown known that some known strongly balanced uniform repeated measurements designs can be modified to obtain optimal designs for this problem. Some other methods of finding optimal designs are also given.     

The analysis of mixed and random effects models for equireplicate variance-balanced block designs

Equirephcate variance-balanced block designs possess many desirable properties and include several important subclasses of designs, such as balanced incomplete block designs. However, while attention has been paid to the derivation of properties and the construction of these designs, methods of analyzing experiments using these designs have not been developed completely. Thus, we consider models appropriate to these designs, construct test statistics for basic hypotheses and derive the distributions for these statistics. Four additive models that include all of the possible combinations of fixed and random effects are examined. The analyses are generalizations of the analyses for balanced incomplete block designs, and include the intra-block, intra-treatment and inter-block analyses, Estimators of fixed treatment effects and their distributions also are given.     

On sum composition of fractional factorial designs

Combinatorial extension and composition methods have been extensively used in the construction of block designs. One of the composition methods, namely the direct product or Kronecker product method was utilized by Chakravarti [1956] to produce certain types of fractional factorial designs. The present paper shows how the direct sum operation can be utilized in obtaining from initial fractional factorial designs for two separate symmetrical factorials a fractional factorial design for the corresponding asymmetrical factorial. Specifically, we provide some results which are useful in the construction of non-singular fractional factorial designs via the direct sum composition method. In addition a modified direct sum method is discussed and the consequences of imposing orthogonality are explored.     

On a paper by kageyama and mohan

Kageyama Mohan (1984) have presented three methods of constructing new incomplete block designs from balanced incomplete block designs, They raise questions about the designs which come from each of their methods, These questions are answered, Another series of group divisible designs is derived as a special case of their second method.     

Equivalence of factorial designs with qualitative and quantitative factors

Two symmetric fractional factorial designs with qualitative and quantitative factors are equivalent if the design matrix of one can be obtained from the design matrix of the other by row and column permutations, relabeling of the levels of the qualitative factors and reversal of the levels of the quantitative factors. In this paper, necessary and sufficient methods of determining equivalence of any two symmetric designs with both types of factors are given. An algorithm used to check equivalence or non-equivalence is evaluated. If two designs are equivalent the algorithm gives a set of permutations which map one design to the other. Fast screening methods for non-equivalence are considered. Extensions of results to asymmetric fractional factorial designs with qualitative and quantitative factors are discussed.     

A survey and evaluation of methods for determination of combinatorial equivalence of factorial designs

Equivalent factorial designs have identical statistical properties for estimation of factorial contrasts and for model fitting. Non-equivalent designs, however, may have the same statistical properties under one particular model but different properties under a different model. In this paper, we describe known methods for the determination of equivalence or non-equivalence of two-level factorial designs, whether they be regular factorial designs, non-regular orthogonal arrays, or have no particular structure. In addition, we evaluate a number of potential fast screening methods for detecting non-equivalence of designs. Although the paper concentrates mainly on symmetric designs with factors at two levels, we also evaluate methods of determining combinatorial equivalence and non-equivalence of three-level designs and indicate extensions to larger numbers of levels and to asymmetric designs.     

A REVIEW OF BOUNDS FOR THE EFFICIENCY FACTOR OF BLOCK DESIGNS

This paper draws together bounds for the efficiency factor of block designs, starting with the papers of Conniffe & Stone (1974) and Williams & Patterson (1977). By extending the methods of Jarrett (1983), firstly to cover supercomplete block designs and then to cover resolvable designs, a set of bounds is obtained which provides the best current bounds for any block design with equal replication and equal block size, including resolvable designs and two-replicate resolvable designs as special cases. The bounds given for non-resolvable designs apply strictly only to designs which are either regular-graph (John & Mitchell, 1977) or whose duals are regular-graph. It is conjectured (John & Williams, 1982) that they are in fact global bounds. Similar qualifications apply to the bounds for resolvable designs.     

D-optimal designs with minimal and nearly minimal number of units

D-optimal designs are identified in classes of connected block designs with fixed block size when the number of experimental units is one or two more than the minimal number required for the design to be connected. An application of one of these results is made to identify D-optimal designs in a class of minimally connected row-column designs. Graph-theoretic methods are employed to arrive at the optimality results.     

Constructions of group divisible designs and related combinatorial structures

Several methods of constructing group divisible (GD) designs are given by use of rectangular designs and nested balanced incomplete block designs. The GD designs obtained here are rather large, but as series they appear to be new. In the process, some series of rectangular designs, balanced arrays, and orthogonal arrays are also provided.     

Constructions of partially efficiency-balanced designs and their analysis

Partially Efficiency-Balanced (PEB) designs were introduced by Puri and Nigam $year:1977. These designs may be particularly useful for bio-assays and factorial experiments and have a very simple analysis. In the present paper, we give several new systematic procedures of constructing PEB designs with varying replications. A number of practical series of PEB designs are presented. We shall also pre- sent the methods of analysing these designs produced here.     

Restricted region designs for multifactor mixture experiments

Designs for multifactor mixture experiments in which the component proportions are restricted by some specified lower and upper limits, are called restricted region designs (RRD) for multifactor mixture experiments. In this paper (i) a method of construction of designs for multifactor mixture experiments and (ii) two methods of constructing RRD for multifactor mixture experiments are described. Examples to illustrate the methods of construction have been given.     

On the Construction of Nearest–Neighbour Balanced Row–Column Designs

Nearest–neighbour balance is considered a desirable property for an experiment to possess in situations where experimental units are influenced by their neighbours. This paper introduces a measure of the degree of nearest–neighbour balance of a design. The measure is used in an algorithm which generates nearest–neighbour balanced designs and is readily modified to obtain designs with various types of nearest–neighbour balance. Nearest–neighbour balanced designs are produced for a wide class of parameter settings, and in particular for those settings for which such designs cannot be found by existing direct combinatorial methods. In addition, designs with unequal row and column sizes, and designs with border plots are constructed using the approach presented here.