The EADGENE Microarray Data Analysis Workshop (Open Access publication)

Genetics Selection Evolution

Luc Janss⁷  Haisheng Nie²  Miha Lavrič^1,10  Peter Dovč^1,10  Johanne C Detilleux^1,12  Rodrigue Closset^1,13  Eva Pérez-Reinado⁸  Mónica Pérez-Alegre⁸  Ángeles Jiménez-Marín⁸  David Waddington^1,12  Daphne Mouzaki^1,12  Kirsty Jensen^1,12  Hans-Martin Seyfert⁹  Ronald M Brunner⁹  Alessandra Stella¹  Roberto Malinverni¹  Michael D Baron⁶  Magali San Cristobal³  Kim-Anh Lê Cao⁵  Céline Delmas³  Guillemette Marot^1,11  Peter Sørensen⁷  Li Jiang⁷  Henrik Hornshøj⁷  Jakob Hedegaard⁷  Bart Buitenhuis⁷  Marco H Pool⁴  Ina Hulsegge⁴  Caroline Channing^1,12  Michael Watson^1,14  Mogens Sandø Lund⁷  Florence Jaffrézic^1,11  Dirk-Jan de Koning^1,12 

[1] Parco Tecnologico Padano (PTP), Lodi, Italy;Wageningen University and Research Centre, Wageningen, The Netherlands;INRA, UMR444, Castanet-Tolosan, France;Animal Sciences Group Wageningen UR, Lelystad, The Netherlands;Université Paul Sabatier, Toulouse, France;Institute for Animal Health, Pirbright, UK;University of Aarhus, Tjele, Denmark;University of Córdoba, Córdoba, Spain;Research Institute for the Biology of Farm Animals, Dummerstorf, Germany;University of Ljubljana, Ljubljana, Slovenia;INRA, UR337, Jouy-en-Josas, France;Roslin Institute, Roslin, UK;University of Liege, Liege, Belgium;Institute for Animal Health, Compton, UK

关键词: statistical analysis;    two colour microarray;    gene expression;   

Others  :  1093950
DOI  :  10.1186/1297-9686-39-6-621

 received in 2007-05-10, accepted in 2007-07-03,  发布年份 2007

【 摘 要 】

Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from 10 countries performed and discussed the statistical analyses of real and simulated 2-colour microarray data that were distributed among participants. The real data consisted of 48 microarrays from a disease challenge experiment in dairy cattle, while the simulated data consisted of 10 microarrays from a direct comparison of two treatments (dye-balanced). While there was broader agreement with regards to methods of microarray normalisation and significance testing, there were major differences with regards to quality control. The quality control approaches varied from none, through using statistical weights, to omitting a large number of spots or omitting entire slides. Surprisingly, these very different approaches gave quite similar results when applied to the simulated data, although not all participating groups analysed both real and simulated data. The workshop was very successful in facilitating interaction between scientists with a diverse background but a common interest in microarray analyses.

【 授权许可】

   
2007 INRA, EDP Sciences