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Each row of the spreadsheet (Figure 1) corresponds to a single sample. The first column is the names of the .idat files and the remaining columns are the array probes. The table values are β-values, which correspond to the percentage methylation at each site. A β-value is 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).
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SubtitleText | Spreadsheet 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) |
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AnchorName | top level spreadsheet |
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Before we can perform any analysis, the study samples need to be organized into their experimental groups.
- Select Add Sample Attributes from the Import section of the Illumina BeadArray Methylation workflow
- Select Add a Categorical Attribute from the Add Sample Attributes dialog (Figure 2)
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SubtitleText | Adding 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 |
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AnchorName | add sample attributes selector |
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The Create categorical attribute dialog allows us to create groups for a categorical attribute. By default, two groups are created, but additional groups can be added.
- Set Attribute name: to Cell Type
- Rename the groups B cells and LCLs
- Drag and drop the samples from the Unassigned list to their groups as listed in the table below
Sample ID | Cell Type |
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GSM2452106_200483200025_R04C01 | B cells |
GSM2452107_200483200021_R01C01 | B cells |
GSM2452108_200483200021_R02C01 | B cells |
GSM2452109_200483200025_R06C01 | B cells |
GSM2452110_200483200025_R07C01 | B cells |
GSM2452111_200483200021_R08C01 | B cells |
GSM2452112_200483200021_R06C01 | B cells |
GSM2452113_200483200021_R04C01 | B cells |
GSM2452114_200483200025_R01C01 | LCLs |
GSM2452115_200483200025_R03C01 | LCLs |
GSM2452116_200483200021_R03C01 | LCLs |
GSM2452117_200483200025_R05C01 | LCLs |
GSM2452118_200483200025_R02C01 | LCLs |
GSM2452119_200483200021_R07C01 | LCLs |
GSM2452120_200483200021_R05C01 | LCLs |
GSM2452121_200483200025_R08C01 | LCLs |
There should now be two groups with eight samples in each group (Figure 3).
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SubtitleText | Adding Cell Type attribute as a categorical group |
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AnchorName | State attribute |
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- Select OK
- Select Yes from the Add another categorical attribute dialog
- Set Attribute name: to Gender
- Rename the groups Male and Female
- Drag and drop the samples from the Unassigned list to their groups as listed in the table below
Sample ID | Gender |
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GSM2452106_200483200025_R04C01 | Female |
GSM2452107_200483200021_R01C01 | Female |
GSM2452108_200483200021_R02C01 | Male |
GSM2452109_200483200025_R06C01 | Female |
GSM2452110_200483200025_R07C01 | Female |
GSM2452111_200483200021_R08C01 | Female |
GSM2452112_200483200021_R06C01 | Female |
GSM2452113_200483200021_R04C01 | Male |
GSM2452114_200483200025_R01C01 | Female |
GSM2452115_200483200025_R03C01 | Female |
GSM2452116_200483200021_R03C01 | Male |
GSM2452117_200483200025_R05C01 | Female |
GSM2452118_200483200025_R02C01 | Female |
GSM2452119_200483200021_R07C01 | Female |
GSM2452120_200483200021_R05C01 | Female |
GSM2452121_200483200025_R08C01 | Male |
There should now be two groups with four samples in Male and twelve samples in Female (Figure 4).
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SubtitleText | Adding Gender attribute as a categorical group |
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AnchorName | State attribute |
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- Select OK
- Select No from the Add another categorical attribute dialog
- Select Yes to save the spreadsheet
Two new columns have been added to spreadsheet 1 (Methylation) with the cell type and gender of each sample (Figure 5).
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SubtitleText | Annotated beta values spreadsheet |
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AnchorName | Annotated spreadsheet |
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