Genomics Suite Documentation

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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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SubtitleTextAdding sample attributes. Adding Attributes from an Existing Column can be used to split file names into sections, based on delimiters (e.g. _, -, space etc.). Adding a Numeric or Categorical Attribute enables the user to manually specify sample attributes
AnchorNameadd sample attributes selector

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The following dialog is Create Categorical Attribute (Figure 3). The Attribute name filed specifies the name of the new column (attribute), while the groups (levels of the attribute) are specified in the Group Name fields. By default, two groups are created, but additional ones can be added using the New Group button. Finally, drag and drop the samples from the Unassigned list to their matching groups. 

 

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SubtitleTextCreate Categorical Attribute is used to define new groups and assign samples to them. The name of new column (attribute) is specified in the Attribute name field, group labels (attribute levels) are specified in the Group Name fields. To assign samples to groups, use drag and drop (to select more than one, use Ctrl or Shift buttons)
AnchorNameassigning samples to groups

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For this analysis, specify Attribute name as HPSC and then create the groups and add samples to them using the table below.

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