The EADGENE Microarray Data Analysis Workshop (open access publication).
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.
de Koning
Dirk-Jan
DJ
Roslin Institute, Roslin, UK. DJ.dekoning@bbsrc.ac.uk
Jaffrézic
Florence
F
Lund
Mogens Sandø
MS
Watson
Michael
M
Channing
Caroline
C
Hulsegge
Ina
I
Pool
Marco H
MH
Buitenhuis
Bart
B
Hedegaard
Jakob
J
Hornshøj
Henrik
H
Jiang
Li
L
Sørensen
Peter
P
Marot
Guillemette
G
Delmas
Céline
C
Lê Cao
Kim-Anh
KA
San Cristobal
Magali
M
Baron
Michael D
MD
Malinverni
Roberto
R
Stella
Alessandra
A
Brunner
Ronald M
RM
Seyfert
Hans-Martin
HM
Jensen
Kirsty
K
Mouzaki
Daphne
D
Waddington
David
D
Jiménez-Marín
Angeles
A
Pérez-Alegre
Mónica
M
Pérez-Reinado
Eva
E
Closset
Rodrigue
R
Detilleux
Johanne C
JC
Dovc
Peter
P
Lavric
Miha
M
Nie
Haisheng
H
Janss
Luc
L
D000818:Animals; D000829:Animals, Domestic / Q000235:genetics; D002417:Cattle; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D004927:Escherichia coli Infections / Q000235:genetics / Q000662:veterinary; D005060:Europe; D005260:Female; D020869:Gene Expression Profiling / Q000592:standards / Q000706:statistics & numerical data; D054884:Host-Pathogen Interactions / Q000235:genetics; D008414:Mastitis, Bovine / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards / Q000706:statistics & numerical data*; D011786:Quality Control; D013203:Staphylococcal Infections / Q000235:genetics / Q000662:veterinary