Enrichment or depletion of a GO category within a class of genes: which testReportar como inadecuado

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* Corresponding author 1 ESA - Equipe de Statistique Appliquée 2 Laboratoire de Neurobiologie et Diversité Cellulaire

Abstract : Motivation: A number of available program packages determine the significant enrichments and-or depletions of GO categories among a class of genes of interest. Whereas a correct formulation of the prob-lem leads to a single exact null distribution, these GO tools use a large variety of statistical tests whose denominations often do not clarify the underlying p-value computations. Summary: We review the different formulations of the problem and the tests they lead to: the binomial, χ2, equality of two probabilities, Fisher-s exact, and hypergeometric tests. We clarify the relation-ships existing between these tests, in particular the equivalence between the hypergeometric test and Fisher-s exact test. We recall that the other tests are valid only for large samples, the test of equal-ity of two probabilities and the χ2 test being equivalent. We discuss the appropriateness of one- and two-sided p-values, as well as some discreteness and conservatism issues.

Keywords : p-value. GO category Fisher-s exact test hypergeometric test p-value

Autor: Isabelle Rivals - Léon Personnaz - Lieng Taing - Potier Marie-Claude -

Fuente: https://hal.archives-ouvertes.fr/


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