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Evaluation of external RNA controls for the assessment of microarray performance

Weida Tong, Anne Bergstrom Lucas, Richard Shippy, Xiaohui Fan, Hong Fang, Huixiao Hong, Michael S Orr, Tzu-Ming Chu, Xu Guo, Patrick J Collins, Yongming Andrew Sun, Sue-Jane Wang, Wenjun Bao, Russell D Wolfinger, Svetlana Shchegrova, Lei Guo, Janet A Warrington & Leming Shi

Supplementary Fig. 1 (doc 100K)
Comparison of the correlation coefficients for each assay from the lines fit through the expected versus observed log10 ratios in Figure 4.

Supplementary Fig. 2 (doc 90K)
The tERC signal intensity across different RNA samples.

Supplementary Fig. 3 (doc 140K)
The effect of normalization methods on the tERC performance behavior across the same RNA samples illustrated in Supplementary Figure 2.

Supplementary Fig. 4 (doc 35K)
Observed log10 ratios for the AGL tERCs that are spiked in at intended 1:1 ratios in the Two-Color hybridization samples.

Supplementary Fig. 5 (doc 110K)
Correlation Assuming Percent Brain is Changed to mRNA Differences Between in the Samples.

Supplementary Fig. 6 (doc 35K)
The cERC signal intensity (y-axis) was compared across the four different RNA samples (A, B, C and D) for the ABI (top graph) and AFX (bottom graph) platforms.

Supplementary Fig. 7 (doc 70K)
The effect of normalization method on the sample independency of the cERC signal intensity (y-axis) for the AFX microarray platform.

Supplementary Fig. 8 (doc 160K)
Hierarchical cluster analysis for the One-Color AG1 platform based on either the tERC probes (A) or the biological probes (B).

Supplementary Fig. 9 (doc 270K)
Full Concentration-Response Curves for tERCs on the Agilent microarray platform.

Supplementary Table 1 (doc 50K)
Summary of cERC Concentration and tERC Molar Ratio Used for Plotting Concentration-Response Curves in Figure 1.

Supplementary Table 2 (doc 1950K)
Summary of statistical results presented in Figure 3.

Supplementary Table 3 (doc 40K)
Summary of statistical results presented in Figure 5.

Supplementary Table 4 (doc 40K)
Summary of tERC Concentration and Expected Two-Color Ratios for the AGL Platform.

Supplementary Methods (zip 2MB)

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