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Figure 1 | BMC Research Notes

Figure 1

From: Quantitative cross-validation and content analysis of the 450k DNA methylation array from Illumina, Inc.

Figure 1

Cross-validation of 450k methylation array and quantitative pyrosequencing. Shown are scatter plots for the methylation values obtained by pyrosequencing (x-axis) and the β-values obtained from the 450k array for identical CpG sites. A) cell lines (Spearman r = 0.88, linear regression r2 = 0.89, slope: 0.89, 95% confidence interval: 0.86 – 0.93), B) primary human tumor tissues (Spearman r = 0.85, linear regression r2 = 0.77, slope: 0.86, 95% confidence interval: 0.81 – 0.91). Each dot in the figure represents the comparison of % methylation according to pyrosequencing versus the β-value for a single CpG site in one sample. C) and D) corresponding Bland-Altman plots. The difference between both methods for every individual measurement is plotted against the mean of both methods. The mean of the differences +/− two times the standard deviation denotes the 95% range for the limits of agreement (marked by the horizontal dotted lines). For the construction of these plots the β-values have been multiplied by the factor 100 in order to obtained data sets of the same size range. The coordinates of the individual CpG sites analyzed in this comparison are compiled in Additional file 3

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