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.
Roslin Institute, Roslin, UK. DJ.dekoning@bbsrc.ac.uk
Dirk-Jan
DJ
de Koning
Florence
F
Jaffrézic
Mogens Sandø
MS
Lund
Michael
M
Watson
Caroline
C
Channing
Ina
I
Hulsegge
Marco H
MH
Pool
Bart
B
Buitenhuis
Jakob
J
Hedegaard
Henrik
H
Hornshøj
Li
L
Jiang
Peter
P
Sørensen
Guillemette
G
Marot
Céline
C
Delmas
Kim-Anh
KA
Lê Cao
Magali
M
San Cristobal
Michael D
MD
Baron
Roberto
R
Malinverni
Alessandra
A
Stella
Ronald M
RM
Brunner
Hans-Martin
HM
Seyfert
Kirsty
K
Jensen
Daphne
D
Mouzaki
David
D
Waddington
Angeles
A
Jiménez-Marín
Mónica
M
Pérez-Alegre
Eva
E
Pérez-Reinado
Rodrigue
R
Closset
Johanne C
JC
Detilleux
Peter
P
Dovc
Miha
M
Lavric
Haisheng
H
Nie
Luc
L
Janss
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