Multiple-laboratory comparison of microarray platforms.
Microarray technology is a powerful tool for measuring RNA expression for thousands of genes at once. Various studies have been published comparing competing platforms with mixed results: some find agreement, others do not. As the number of researchers starting to use microarrays and the number of cross-platform meta-analysis studies rapidly increases, appropriate platform assessments become more important. Here we present results from a comparison study that offers important improvements over those previously described in the literature. In particular, we noticed that none of the previously published papers consider differences between labs. For this study, a consortium of ten laboratories from the Washington, DC-Baltimore, USA, area was formed to compare data obtained from three widely used platforms using identical RNA samples. We used appropriate statistical analysis to demonstrate that there are relatively large differences in data obtained in labs using the same platform, but that the results from the best-performing labs agree rather well.
Irizarry
Rafael A
RA
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA. rafa@jhu.edu
Warren
Daniel
D
Spencer
Forrest
F
Kim
Irene F
IF
Biswal
Shyam
S
Frank
Bryan C
BC
Gabrielson
Edward
E
Garcia
Joe G N
JG
Geoghegan
Joel
J
Germino
Gregory
G
Griffin
Constance
C
Hilmer
Sara C
SC
Hoffman
Eric
E
Jedlicka
Anne E
AE
Kawasaki
Ernest
E
Martínez-Murillo
Francisco
F
Morsberger
Laura
L
Lee
Hannah
H
Petersen
David
D
Quackenbush
John
J
Scott
Alan
A
Wilson
Michael
M
Yang
Yanqin
Y
Ye
Shui Qing
SQ
Yu
Wayne
W
D015142:Baltimore; D004219:District of Columbia; D020869:Gene Expression Profiling / Q000592:standards; D006801:Humans; D007753:Laboratories / Q000592:standards; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards*; D015203:Reproducibility of Results