In this paper a correction of SGoF multitesting method for dependent tests is introduced. The correction is based in the beta-binomial model, and therefore the new method is called Beta-Binomial SGoF (or BB-SGoF). Main properties of the new method are established, and its practical...

Motivation: Assessment of gene expression on spotted microarrays is based on measurement of fluorescence intensity emitted by hybridized spots. Unfortunately, quantifying fluorescence intensity from hybridized spots does not always correctly reflect gene expression level. Low gene expression...

We study exact tests for (2 x 2) and (2 x 3) contingency tables, in particular exact chi-squared tests and exact tests of Fisher type. In practice, these tests are typically carried out without randomization, leading to reproducible results but not exhausting the significance level. We discuss...

Clustering of gene expression data is often done with the latent aim of dimension reduction, by finding groups of genes that have a common response to potentially unknown stimuli. However, what is poorly understood to date is the behaviour of a low dimensional signal embedded in high dimensions....

In many published genome-wide association studies (GWAS), the top few strongly associated variants are often located in or near known genes. This observation raises the more general hypothesis that variants nominally associated with a phenotype are more likely to overlap genes than those not...

Applications on inference of biological networks have raised a strong interest in the problem of graph estimation in high-dimensional Gaussian graphical models. To handle this problem, we propose a two-stage procedure which first builds a family of candidate graphs from the data, and then...

In cancer clinical proteomics, MALDI and SELDI profiling are used to search for biomarkers of potentially curable early-stage disease. A given number of samples must be analysed in order to detect clinically relevant differences between cancers and controls, with adequate statistical power. From...

Most approaches for analyzing ChIP-Seq data are focused on inferring exact protein binding sites from a single library. However, frequently multiple ChIP-Seq libraries derived from differing cell lines or tissue types from the same individual may be available. In such a situation, a separate...

Hypotheses tests in bioinformatics can often be set in a tree structure in a very natural way, e.g. when tests are performed at probe, gene, and chromosome level. Exploiting this graph structure in a multiple testing procedure may result in a gain in power or increased interpretability of the...

The general availability of reliable and affordable genotyping technology has enabled genetic association studies to move beyond small case-control studies to large prospective studies. For prospective studies, genetic information can be integrated into the analysis via haplotypes, with focus on...