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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.

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Figure 1: Volcano plots depicting estimated fold change (log2, x-axis) and statistical significance (−log10 P value, y-axis).
Figure 2: Comparison of log2 fold-change estimate results from three different modeling approaches for the three different platforms.
Figure 3: Comparison of negative log10 P-value estimate results from three different modeling approaches for the three different platforms.
Figure 4: Comparison of Agilent one-color and two-color data with TaqMan assay data.

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The authors thank the MicroArray Quality Control (MAQC) consortium for generating the large data sets used in this study. E.K.L. and P.H. acknowledge the Advanced Technology Program of the National Institute of Standards and Technology, whose generous support provided partial funding of this research (70NANB2H3009).

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Correspondence to Tucker A Patterson.

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Competing interests

S.B.F.-S., P.J.C. and L.Z. declare competing financial interests. While engaged in this research project, they were employed by two separate companies that manufacture microarrays. These two companies provided two of the three platforms used in this study.

Supplementary information

Supplementary Fig. 1

Example scatter plot matrices from each platform (PDF 114 kb)

Supplementary Fig. 2

Comparison of B/A ratios for Agilent one-color and two-color designs (Site 1) (PDF 115 kb)

Supplementary Fig. 3

Comparison of the normalization procedures on two-color TeleChem data: Lowess_Medium Scaling (LO_MS) versus Medium Scaling_Lowess (MS_LO) (PDF 19 kb)

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Patterson, T., Lobenhofer, E., Fulmer-Smentek, S. et al. Performance comparison of one-color and two-color platforms within the Microarray Quality Control (MAQC) project. Nat Biotechnol 24, 1140–1150 (2006).

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