Genomics Suite Documentation

PGS Documentation

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Numbered figure captions
SubtitleTextSpreadsheet after .idat file import: samples on rows (Sample IDs are based on file names), probes on columns, cell values are functionally normalized beta values (default settings)
AnchorNametop level spreadsheet

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As discussed in the previous chapter, the values in the cells are normalized β-values, which correspond to the percentage of methylation at each site and are calculated as the ratio of methylated probe intensity over the overall intensity at each site (the overall intensity is the sum of methylated and unmethylated probe intensities). An alternative metric for measurement of methlyation levels are M-values. β-values can be easily converted to M-values using the following equation:

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