Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project.
Microarray-based expression profiling experiments typically use either a one-color or a two-color design to measure mRNA abundance. The validity of each approach has been amply demonstrated. Here we provide a simultaneous comparison of results from one- and two-color labeling designs, using two independent RNA samples from the Microarray Quality Control (MAQC) project, tested on each of three different microarray platforms. The data were evaluated in terms of reproducibility, specificity, sensitivity and accuracy to determine if the two approaches provide comparable results. For each of the three microarray platforms tested, the results show good agreement with high correlation coefficients and high concordance of differentially expressed gene lists within each platform. Cumulatively, these comparisons indicate that data quality is essentially equivalent between the one- and two-color approaches and strongly suggest that this variable need not be a primary factor in decisions regarding experimental microarray design.
Patterson
Tucker A
TA
National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Rd., Jefferson, Arkansas 72079, USA. tucker.patterson@fda.hhs.gov
Lobenhofer
Edward K
EK
Fulmer-Smentek
Stephanie B
SB
Collins
Patrick J
PJ
Chu
Tzu-Ming
TM
Bao
Wenjun
W
Fang
Hong
H
Kawasaki
Ernest S
ES
Hager
Janet
J
Tikhonova
Irina R
IR
Walker
Stephen J
SJ
Zhang
Liang
L
Hurban
Patrick
P
de Longueville
Francoise
F
Fuscoe
James C
JC
Tong
Weida
W
Shi
Leming
L
Wolfinger
Russell D
RD
D004867:Equipment Design; D019544:Equipment Failure Analysis; D020869:Gene Expression Profiling / Q000295:instrumentation* / Q000379:methods; D017404:In Situ Hybridization, Fluorescence / Q000295:instrumentation*; D036641:Microscopy, Fluorescence, Multiphoton / Q000295:instrumentation* / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation*; D011785:Quality Assurance, Health Care / Q000379:methods*; D011786:Quality Control; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013050:Spectrometry, Fluorescence / Q000295:instrumentation* / Q000379:methods; D014481:United States