Performance comparison of one-color and two-color platforms within the Microarray Quality Control (MAQC) project

• Published in: Nature biotechnology Vol. 24; no. 9; pp. 1140 - 1150
• Main Authors: Patterson, Tucker A, Lobenhofer, Edward K, Fulmer-Smentek, Stephanie B, Collins, Patrick J, Chu, Tzu-Ming, Bao, Wenjun, Fang, Hong, Kawasaki, Ernest S, Hager, Janet, Tikhonova, Irina R, Walker, Stephen J, Zhang, Liang, Hurban, Patrick, de Longueville, Francoise, Fuscoe, James C, Tong, Weida, Shi, Leming, Wolfinger, Russell D
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.09.2006; Nature Publishing Group
• Subjects: Agriculture; analysis; Bioinformatics; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Color; Comparative studies; Correlation coefficient; Design; Design of experiments; Equipment Design; Equipment Failure Analysis; Gene expression; Gene Expression Profiling - instrumentation; Gene Expression Profiling - methods; In Situ Hybridization, Fluorescence - instrumentation; Life Sciences; Microscopy, Fluorescence, Multiphoton - instrumentation; Microscopy, Fluorescence, Multiphoton - methods; Oligonucleotide Array Sequence Analysis - instrumentation; Quality Assurance, Health Care - methods; Quality Control; Reproducibility of Results; Ribonucleic acid; RNA; Sensitivity and Specificity; Spectrometry, Fluorescence - instrumentation; Spectrometry, Fluorescence - methods; United States; United States
• ISSN: 1087-0156; 1546-1696
• DOI: 10.1038/nbt1242

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.