sdef: an R package to synthesize lists of significant features in related experiments

Background: In microarray studies researchers are often interested in the comparison of relevant quantities between two or more similar experiments, involving different treatments, tissues, or species. Typically each experiment reports measures of significance (e.g. p-values) or other measures that rank its features (e.g genes). Our objective is to find a list of features that are significant in all experiments, to be further investigated. In this paper we present an R package called sdef, that allows the user to quantify the evidence of communality between the experiments using previously proposed statistical methods based on the ranked lists of p-values. sdef implements two approaches that address this objective: the first is a permutation test of the maximal ratio of observed to expected common features under the hypothesis of independence between the experiments. The second approach, set in a Bayesian framework, is more flexible as it takes into account the uncertainty on the numb...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Marta Blangiardo, Alberto Cassese, Sylvia Richardson
• Keywords: BMCBI 2010, E.g Genes, Microarray Studies Researchers, Relevant Quantities