Repeatability of published microarray gene expression analyses. Export

@article{citeulike:3973376, 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.}, author = {Ioannidis, John P. A. and Allison, David B. and Ball, Catherine A. and Coulibaly, Issa and Cui, Xiangqin and Culhane, Aedin C. and Falchi, Mario and Furlanello, Cesare and Game, Laurence and Jurman, Giuseppe and Mangion, Jon and Mehta, Tapan and Nitzberg, Michael and Page, Grier P. and Petretto, Enrico and van Noort, Vera}, citeulike-article-id = {3973376}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/ng.295}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/ng.295}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19174838}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19174838}, day = {28}, doi = {10.1038/ng.295}, issn = {1546-1718}, journal = {Nature genetics}, keywords = {analysis, data-analysis, expression, gene, methods, microarray, review}, month = {January}, number = {2}, pages = {149--155}, posted-at = {2009-10-12 17:13:03}, priority = {2}, publisher = {Nature Publishing Group}, title = {Repeatability of published microarray gene expression analyses.}, url = {http://dx.doi.org/10.1038/ng.295}, volume = {41}, year = {2009} }

TY - JOUR ID - citeulike:3973376 L3 - citeulike-article-id:3973376 N2 - 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. IS - 2 JF - Nature genetics SN - 1546-1718 EP - 155 TI - Repeatability of published microarray gene expression analyses. PB - Nature Publishing Group VL - 41 SP - 149 KW - analysis KW - data-analysis KW - expression KW - gene KW - methods KW - microarray KW - review AU - Ioannidis, John AU - Allison, David AU - Ball, Catherine AU - Coulibaly, Issa AU - Cui, Xiangqin AU - Culhane, Aedin AU - Falchi, Mario AU - Furlanello, Cesare AU - Game, Laurence AU - Jurman, Giuseppe AU - Mangion, Jon AU - Mehta, Tapan AU - Nitzberg, Michael AU - Page, Grier AU - Petretto, Enrico AU - van Noort, Vera PY - 2009/01/28/ UR - http://dx.doi.org/10.1038/ng.295 ER -