Standardizing global gene expression analysis between laboratories and across platforms.
To facilitate collaborative research efforts between multi-investigator teams using DNA microarrays, we identified sources of error and data variability between laboratories and across microarray platforms, and methods to accommodate this variability. RNA expression data were generated in seven laboratories, which compared two standard RNA samples using 12 microarray platforms. At least two standard microarray types (one spotted, one commercial) were used by all laboratories. Reproducibility for most platforms within any laboratory was typically good, but reproducibility between platforms and across laboratories was generally poor. Reproducibility between laboratories increased markedly when standardized protocols were implemented for RNA labeling, hybridization, microarray processing, data acquisition and data normalization. Reproducibility was highest when analysis was based on biological themes defined by enriched Gene Ontology (GO) categories. These findings indicate that microarray results can be comparable across multiple laboratories, especially when a common platform and set of procedures are used.
Bammler
Theodore
T
Beyer
Richard P
RP
Bhattacharya
Sanchita
S
Boorman
Gary A
GA
Boyles
Abee
A
Bradford
Blair U
BU
Bumgarner
Roger E
RE
Bushel
Pierre R
PR
Chaturvedi
Kabir
K
Choi
Dongseok
D
Cunningham
Michael L
ML
Deng
Shibing
S
Dressman
Holly K
HK
Fannin
Rickie D
RD
Farin
Fredrico M
FM
Freedman
Jonathan H
JH
Fry
Rebecca C
RC
Harper
Angel
A
Humble
Michael C
MC
Hurban
Patrick
P
Kavanagh
Terrance J
TJ
Kaufmann
William K
WK
Kerr
Kathleen F
KF
Jing
Li
L
Lapidus
Jodi A
JA
Lasarev
Michael R
MR
Li
Jianying
J
Li
Yi-Ju
YJ
Lobenhofer
Edward K
EK
Lu
Xinfang
X
Malek
Renae L
RL
Milton
Sean
S
Nagalla
Srinivasa R
SR
O'malley
Jean P
JP
Palmer
Valerie S
VS
Pattee
Patrick
P
Paules
Richard S
RS
Perou
Charles M
CM
Phillips
Ken
K
Qin
Li-Xuan
LX
Qiu
Yang
Y
Quigley
Sean D
SD
Rodland
Matthew
M
Rusyn
Ivan
I
Samson
Leona D
LD
Schwartz
David A
DA
Shi
Yan
Y
Shin
Jung-Lim
JL
Sieber
Stella O
SO
Slifer
Susan
S
Speer
Marcy C
MC
Spencer
Peter S
PS
Sproles
Dean I
DI
Swenberg
James A
JA
Suk
William A
WA
Sullivan
Robert C
RC
Tian
Ru
R
Tennant
Raymond W
RW
Todd
Signe A
SA
Tucker
Charles J
CJ
Van Houten
Bennett
B
Weis
Brenda K
BK
Xuan
Shirley
S
Zarbl
Helmut
H
D020869:Gene Expression Profiling / Q000592:standards*; D007753:Laboratories / Q000592:standards; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards*; D015203:Reproducibility of Results