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An alternative way to take a look at the distribution of beta-values is a histogram. 

  • Select Plot Sample Histogram from the QA/QC section of the Illumina BeadArray Methylation workflow to bring up a Histogram tab

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Numbered figure captions
SubtitleTextSample histogram. Each sample is a line, M-beta values are on the horizontal axis and their frequencies on the vertical axis. Two peaks correspond to two probe types (I and II) present on the MethylationEPIC array. Sample colors correspond to a categorical attribute (Cell Type)
AnchorNamesample histogram

 

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