The EADGENE Microarray Data Analysis Workshop (Open Access publication)

de Koning, Dirk-Jan, Jaffrézic, Florence, Lund, Mogens Sandø, Watson, Michael, Channing, Caroline, Hulsegge, Ina, Pool, Marco H., Buitenhuis, Bart, Hedegaard, Jakob, Hornshøj, Henrik, Jiang, Li, Sørensen, Peter, Marot, Guillemette, Delmas, Céline, Lê Cao, Kim-Anh, San Cristobal, Magali, Baron, Michael D., Malinverni, Roberto, Stella, Alessandra, Brunner, Ronald M., Seyfert, Hans-Martin, Jensen, Kirsty, Mouzaki, Daphne, Waddington, David, Jiménez-Marín, Ángeles, Pérez-Alegre, Mónica, Pérez-Reinado, Eva, Closset, Rodrigue, Detilleux, Johanne C., Dovč, Peter, Lavrič, Miha, Nie, Haisheng and Janss, Luc (2007) The EADGENE Microarray Data Analysis Workshop (Open Access publication). Genetics Selection Evolution, 39 6: 621-631. doi:10.1051/gse:2007028

Author de Koning, Dirk-Jan
Jaffrézic, Florence
Lund, Mogens Sandø
Watson, Michael
Channing, Caroline
Hulsegge, Ina
Pool, Marco H.
Buitenhuis, Bart
Hedegaard, Jakob
Hornshøj, Henrik
Jiang, Li
Sørensen, Peter
Marot, Guillemette
Delmas, Céline
Lê Cao, Kim-Anh
San Cristobal, Magali
Baron, Michael D.
Malinverni, Roberto
Stella, Alessandra
Brunner, Ronald M.
Seyfert, Hans-Martin
Jensen, Kirsty
Mouzaki, Daphne
Waddington, David
Jiménez-Marín, Ángeles
Pérez-Alegre, Mónica
Pérez-Reinado, Eva
Closset, Rodrigue
Detilleux, Johanne C.
Dovč, Peter
Lavrič, Miha
Nie, Haisheng
Janss, Luc
Title The EADGENE Microarray Data Analysis Workshop (Open Access publication)
Journal name Genetics Selection Evolution   Check publisher's open access policy
ISSN 0999-193X
Publication date 2007-12
Sub-type Article (original research)
DOI 10.1051/gse:2007028
Open Access Status DOI
Volume 39
Issue 6
Start page 621
End page 631
Total pages 11
Place of publication Paris, France
Publisher EDP Sciences
Language eng
Subject 1001 Agricultural Biotechnology
0104 Statistics
0604 Genetics
Abstract 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. © INRA.
Keyword Gene expression
Statistical analysis
Two colour microarray
Q-Index Code C1
Additional Notes This article is an overview of the data analysis conducted at the EADGENE Microarray Data Analysis Workshop and may contain some editorial comment as well as review of research.

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
Institute for Molecular Bioscience - Publications
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Created: Fri, 28 May 2010, 16:07:54 EST by Mary-Anne Marrington on behalf of Institute for Molecular Bioscience