Microarray studies often need to simultaneously examine thousands of genes to determine which are differentially expressed. One main challenge in those studies is to find suitable multiple testing procedures that provide accurate control of the error rates of interest and meanwhile are most...

Microarray applications for the study of gene expression are becoming accessible for researchers in more and more systems. Applications from field or laboratory experiments are often complicated by the need to superimpose sample pairing for two-color arrays on experimental designs that may...

Pixel saturation occurs when the pixel intensity exceeds the scanner upper threshold of detection and the recorded pixel intensity is then truncated at the threshold. Truncation of the pixel intensity causes the estimates of gene expression (i.e., intensity) to be biased. Microarray experiments...

Partial Least Squares (PLS) dimension reduction is known to give good prediction accuracy in the context of classification with high-dimensional microarray data. In this paper, the classification procedure consisting of PLS dimension reduction and linear discriminant analysis on the new...

Statistical models for spot shapes and signal intensities are used in image analysis of laser scans of microarrays. Most models have essentially been based on the assumption of independent pixel intensity values, but models that allow for spatial correlation among neighbouring pixels can...

Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary biology. We propose a new likelihood based method, COMODE, for identifying structural motifs in DNA sequences. Commonly used methods (e.g. MEME, Gibbs motif sampler) model binding sites...

Microarrays are a tool for measuring the expression levels of a large number of genes simultaneously. In the microarray experiment, however, many undesirable systematic variations are observed. Correct identification and removal of these variations is essential to allow the comparison of...

In this article we describe and discuss implementation of a weighted simulation procedure, importance sampling, in the context of nonparametric linkage analysis. The objective is to estimate genome-wide p-values, i.e. the probability that the maximal linkage score exceeds given thresholds under...

Amplified Fragment Length Polymorphism (AFLP) markers are formed by selective amplification of DNA fragments from digested total genomic DNA. The technique is popular because it is a relatively inexpensive way to produce large numbers of reproducible genetic markers. In this paper, we describe a...

We investigate an important issue of a meta-algorithm for selecting variables in the framework of microarray data. This wrapper method starts from any classification algorithm and weights each variable (i.e. gene) relative to its efficiency for classification. An optimization procedure is then...