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

Tucker A Patterson, Edward K Lobenhofer, Stephanie B Fulmer-Smentek, Patrick J Collins, Tzu-Ming Chu, Wenjun Bao, Hong Fang, Ernest S Kawasaki, Janet Hager, Irina R Tikhonova, Stephen J Walker, Liang Zhang (+6 others)
2006 Nature Biotechnology  
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,
more » ... vity 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. Although microarray technology has now been available for more than ten years 1-3 , many fundamental questions remain about essentially every aspect of its use, including experimental design, data acquisition, data analysis and data interpretation. One of the first decisions encountered
doi:10.1038/nbt1242 pmid:16964228 fatcat:flc6h5nienao3h7ceagi3vmh64