Nature Biotechnology
- 24, 1140 - 1150 (2006)
Published online: 8 September 2006; | doi:10.1038/nbt1242
Performance comparison of one-color and two-color platforms within the Microarray Quality Control (MAQC) projectTucker A Patterson1, Edward K Lobenhofer2, Stephanie B Fulmer-Smentek3, Patrick J Collins3, Tzu-Ming Chu4, Wenjun Bao4, Hong Fang5, Ernest S Kawasaki6, Janet Hager7, Irina R Tikhonova7, Stephen J Walker8, Liang Zhang9, Patrick Hurban2, Francoise de Longueville10, James C Fuscoe1, Weida Tong1, Leming Shi1 & Russell D Wolfinger41
National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Rd., Jefferson, Arkansas 72079, USA. 2
Cogenics, A Division of Clinical Data, 100 Perimeter Park Drive, Suite C, Morrisville, North Carolina 27560, USA. 3
Integrated Biology Solutions, Agilent Technologies, 5301 Stevens Creek Blvd., Santa Clara, California 95052-8059, USA. 4
SAS Institute Inc., SAS Campus Drive, Cary, North Carolina 27513, USA. 5
Division of Bioinformatics, Z-Tech Corporation at NCTR/FDA, 3900 NCTR Rd., Jefferson, Arkansas 72079, USA. 6
NCI Advanced Technology Center, 8717 Grovemont Circle, Bethesda, Maryland 20892-4605, USA. 7
Yale University, W.M. Keck Biotechnology Resource Laboratory, Microarray Resource, 300 George St., Suite 2110, New Haven, Connecticut 06511, USA. 8
Department of Physiology & Pharmacology, Wake Forest University School of Medicine, 115 S. Chestnut St., Winston-Salem, North Carolina 27101, USA. 9
CapitalBio Corporation, 18 Life Science Parkway, Changping District, Beijing 102206, P.R. China. 10
Gene Expression Chips, Eppendorf Array Technologies (EAT), 20, rue du seminaire, 5000 Namur, Belgium.
Correspondence should be addressed to Tucker A Patterson tucker.patterson@fda.hhs.gov 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.
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