title: Repeatability of published microarray gene expression analyses.
abstract: Given the complexity of microarray-based gene expression studies, guidelines encourage transparent design and public data availability. Several journals require public data deposition and several public databases exist. However, not all data are publicly available, and even when available, it is unknown whether the published results are reproducible by independent scientists. Here we evaluated the replication of data analyses in 18 articles on microarray-based gene expression profiling published in Nature Genetics in 2005-2006. One table or figure from each article was independently evaluated by two teams of analysts. We reproduced two analyses in principle and six partially or with some discrepancies; ten could not be reproduced. The main reason for failure to reproduce was data unavailability, and discrepancies were mostly due to incomplete data annotation or specification of data processing and analysis. Repeatability of published microarray studies is apparently limited. More strict publication rules enforcing public data availability and explicit description of data processing and analysis should be considered.
authors.affiliation: Clinical and Molecular Epidemiology Unit, Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina 45110, Greece. jioannid@cc.uoi.gr
authors.forename: John P A
authors.initials: JP
authors.lastname: Ioannidis
authors.forename: David B
authors.initials: DB
authors.lastname: Allison
authors.forename: Catherine A
authors.initials: CA
authors.lastname: Ball
authors.forename: Issa
authors.initials: I
authors.lastname: Coulibaly
authors.forename: Xiangqin
authors.initials: X
authors.lastname: Cui
authors.forename: Aedín C
authors.initials: AC
authors.lastname: Culhane
authors.forename: Mario
authors.initials: M
authors.lastname: Falchi
authors.forename: Cesare
authors.initials: C
authors.lastname: Furlanello
authors.forename: Laurence
authors.initials: L
authors.lastname: Game
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Jurman
authors.forename: Jon
authors.initials: J
authors.lastname: Mangion
authors.forename: Tapan
authors.initials: T
authors.lastname: Mehta
authors.forename: Michael
authors.initials: M
authors.lastname: Nitzberg
authors.forename: Grier P
authors.initials: GP
authors.lastname: Page
authors.forename: Enrico
authors.initials: E
authors.lastname: Petretto
authors.forename: Vera
authors.initials: V
authors.lastname: van Noort
mesh_terms: D000818:Animals; D003627:Data Interpretation, Statistical; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000592:standards*; D055106:Genome-Wide Association Study / Q000592:standards; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards*; D017712:Peer Review, Research; D011642:Publications / Q000592:standards; D015203:Reproducibility of Results