We compare four variants of the reference design for microarray experiments in terms of their relative efficiency. A common reference sample across arrays is the most extensively used variation in practice, but independent samples from a reference group have also been considered in previous...

Simultaneously testing a collection of null hypotheses about a data generating distribution based on a sample of independent and identically distributed observations is a fundamental and important statistical problem involving many applications. In this article we propose a new re-sampling based...

Stochastic dependence between gene expression levels in microarray data is of critical importance for the methods of statistical inference that resort to pooling test statistics across genes. The empirical Bayes methodology in the nonparametric and parametric formulations, as well as closely...

Intensities measurements of spotted microarrays embody many undesirable systematic variations. Very commonly, varying amounts and types of such variations are observed in different arrays. Although various normalization methods have been proposed to remove such systematic effects, it has not...

While scientific research and the methodologies involved have gone through substantial technological evolution the technology involved in the publication of the results of these endeavors has remained relatively stagnant. Publication is largely done in the same manner today as it was fifty years...

We describe statistical inference in continuous time Markov processes of DNA sequences related by a phylogenetic tree. The maximum likelihood estimator can be found by the expectation maximization (EM) algorithm and an expression for the information matrix is also derived. We provide explicit...

We propose a multinomial logistic regression method which permits estimation and likelihood ratio tests for allele effects, their interactions with continuous covariates, and assessment of the degree of population stratification in genetic association studies of case-parent triads. Our approach...

Measurement of the amount of oxidative damage to DNA is one tool that can be used to estimate the beneficial effect of diet on the prevention of colon carcinogenesis. The FLARE assay is a modification of the single-cell gel electrophoresis (Comet) assay, and provides a measure of the 8OHdG...

Gene co-expression networks are increasingly used to explore the system-level functionality of genes. The network construction is conceptually straightforward: nodes represent genes and nodes are connected if the corresponding genes are significantly co-expressed across appropriately chosen...

Gene microarray technology is often used to compare the expression of thousand of genes in two different cell lines. Typically, one does not expect measurable changes in transcription amounts for a large number of genes; furthermore, the noise level of array experiments is rather high in...