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Principal component analysis (PCA) can be invoked on the methylation data to reveal clustering of the samples, but also as a quality control procedure (detection of outliers could point to possible low quality or mislabeled samples). To obtain the PCA plot, switch to the Scatter Plot tab, push Recompute ( ) and from the Color by drop down list select HPSC. Use the Rotate Mode ( )to explore the plot from different angles, as shown in Figure 1.
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