title: Assessing significance in high-throughput experiments by sequential goodness of fit and q-value estimation.
abstract: We developed a new multiple hypothesis testing adjustment called SGoF+ implemented as a sequential goodness of fit metatest which is a modification of a previous algorithm, SGoF, taking advantage of the information of the distribution of p-values in order to fix the rejection region. The new method uses a discriminant rule based on the maximum distance between the uniform distribution of p-values and the observed one, to set the null for a binomial test. This new approach shows a better power/pFDR ratio than SGoF. In fact SGoF+ automatically sets the threshold leading to the maximum power and the minimum false non-discovery rate inside the SGoF' family of algorithms. Additionally, we suggest combining the information provided by SGoF+ with the estimate of the FDR that has been committed when rejecting a given set of nulls. We study different positive false discovery rate, pFDR, estimation methods to combine q-value estimates jointly with the information provided by the SGoF+ method. Simulations suggest that the combination of SGoF+ metatest with the q-value information is an interesting strategy to deal with multiple testing issues. These techniques are provided in the latest version of the SGoF+ software freely available at http://webs.uvigo.es/acraaj/SGoF.htm.
authors.affiliation: Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain. acraaj@uvigo.es
authors.forename: Antonio
authors.initials: A
authors.lastname: Carvajal-Rodriguez
authors.forename: Jacobo
authors.initials: J
authors.lastname: de Uña-Alvarez
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D012984:Software