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- Select the female_only spreadsheet
- Select Transform from the main toolbar
- Select Create Transposed Spreadsheet... from the Transform drop-down menu (Figure 1)
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- Select Sample ID for Column: and numeric for Data Type:
- Select OK
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- Right-click on column 1. ID to bring up the pop-up menu
- Select Insert Annotation
- Select Add as categorical
- Select Infinium_Design_Type and UCSC_CpG_Islands_Name from the Column Configuration options (Figure 2)
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- Select OK to add the Inifinium design type and CpG island name as categorical columns on the spreadsheet
Now we can use the interactive filter to create two separate spreadsheets for type I and type II probes.
- Select ( ) to launch the interactive filter
- Select 2. Infinium_Design_Type from the drop-down menu if not selected by default
- Left-click the type I column to exclude it
- Right-click the temporary spreadsheet in the spreadsheet tree to bring up the pop-up dialog
- Select Clone... (Figure 3)
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- Name the new spreadsheet female_only_typeII_probes
- Select OK
- Save the created spreadsheet, we chose the file name female_only_typeII_probes
- Repeat process to create a spreadsheet for type I probes
The temporary spreadsheet is no longer needed so we can close it.
- Close the temporary spreadsheet by selecting it and selecting ()
We can now use these spreadsheets to generate lists of M values at CpG island regions
- Select spreadsheet female_only_typeII_probes
- Select Stat from the main toolbar
- Select Column Statistics... under Descriptive (Figure 4)
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- Add Mean to the Selected Measure(s) panel
- Select Group By and set it to 3. UCSC_CpG_Islands_Name Name (Figure 5)
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- Select OK
The new temporary spreadsheet (Figure ) has one CpG island region per row (listed in column #2, LevelFigure 6), samples on columns, and the values in the cells represent the mean of M values of all the CpG probes in the region.
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Note the first row, with label “– Mean”. It corresponds to all the probes that map outside of USCS UCSC CpG islands. As it is not needed for the downstream analysis, we will remove it.
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The final step is to transpose the spreadsheet data back to its original orientation.
- Select the female_only_typeII_probes spreadsheet
- Select Transform from the main toolbar
- Select Create Transposed Spreadsheet... from the Transform drop-down menu
- Select Label 2. Level for Column: and numeric for Data Type:
- Select OK
The layout now of the new transposed spreadsheet is as follows: one sample per row with CpG island regions on columns; cell entries correspond to mean methylation status of the region (Figure 7).
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- Select () to save the transposed spreadsheet as female_only_typeII_probes_CpG_islands
- Close the source temporary spreadsheet by selecting it and selecting ()
This spreadsheet can then be used as a starting point for ANOVA and other analyses.
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