Analysis of the real EADGENE data set: Comparison of methods and guidelines for data normalisation and selection of differentially expressed genes (Open Access publication)

F Jaffrézic; DJ De Koning; PJ Boettcher; A Bonnet; B Buitenhuis; R Closset; S Déjean; C Delmas; JC Detilleux; P Dovč; M Duval; JL Foulley; J Hedegaard; H Hornshøj; I Hulsegge; L Janss; K Jensen; L Jiang; M Lavrič; KA Lê Cao; MS Lund; R Malinverni; G Marot; H Nie; W Petzl; MH Pool; C Robert-Granié; M San Cristobal; EM Van Schothorst; HJ Schuberth; P Sørensen; A Stella; G Tosser-Klopp; D Waddington; M Watson; W Yang; H Zerbe; HM Seyfert

Journal article

Analysis of the real EADGENE data set: Comparison of methods and guidelines for data normalisation and selection of differentially expressed genes (Open Access publication)

F Jaffrézic, DJ De Koning, PJ Boettcher, A Bonnet, B Buitenhuis, R Closset, S Déjean, C Delmas, JC Detilleux, P Dovč, M Duval, JL Foulley, J Hedegaard, H Hornshøj, I Hulsegge, L Janss, K Jensen, L Jiang, M Lavrič, KA Lê Cao Show all

Genetics Selection Evolution | BMC | Published : 2007

DOI: 10.1051/gse:2007029

Abstract

A large variety of methods has been proposed in the literature for microarray data analysis. The aim of this paper was to present techniques used by the EADGENE (European Animal Disease Genomics Network of Excellence) WP1.4 participants for data quality control, normalisation and statistical methods for the detection of differentially expressed genes in order to provide some more general data analysis guidelines. All the workshop participants were given a real data set obtained in an EADGENE funded microarray study looking at the gene expression changes following artificial infection with two different mastitis causing bacteria: Escherichia coli and Staphylococcus aureus. It was reassuring t..

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