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Analysis of differentially methylated loci in humans and mice typically includes exclusion of the probes on X and Y chromosomes because of the difficulties caused by the inactivation of one X chromosome in female samples. To filter out probes from the X and Y chromosomes, we first need to annotate the ANOVA spreadsheet with chromosome locations.

  • Right-click on the Gene Symbol column 
  • Select Insert Annotation (Figure 1) 

Figure 1. Adding an annotation column to the ANOVA results
  • Select the Add as categorical option
  • Select CHR (Figure 2)

Figure 2. Adding chromosome location to ANOVA results
  • Select OK to add chromosome as a column in next to 3. Gene Symbol 
  • Select () from the quick action bar to save the ANOVA-1way (ANOVA Results) spreadsheet with the added annotation

Now, we can filter probes by chromosome location.

  • Select () from the quick action bar to invoke the interactive filter
  • Select 4. CHR for Column 

For categorical columns, the interactive filter displays each category of the selected column as a colored bar. For 4. CHR, each bar represents a chromosome with the height of bar representing the number of probes from that chromosome in the selected spreadsheet. To filter out a category, left-click on its bar. Right clicking on a bar will include only the selected category. A pop up balloon will show the category label as you mouse over each bar. 

  • Left-click the and chromosome columns to filter them out (Figure 3)

Figure 3. Using Interactive Filter tool to filter out probes by annotation. When pointed to a categorical column, the Interactive Filter tool summarises the content of the column by a column chart. Left-click to exclude a category (two columns were excluded, so they are grayed out), right-click to include only

The yellow and black bar on the right-hand side of the spreadsheet panel shows the fraction of excluded cells in black and included cells in yellow. Right-clicking this bar brings up an option to clear the filter. 

Now that we have filtered out probes on the X and Y chromosomes, we will create a spreadsheet containing only probes on the autosomes. 

  • Right click on the ANOVA-1way (ANOVAResults) spreadsheet in the spreadsheet tree panel (Figure 4)

Figure 4. Cloning a filtered spreadsheet creates a new spreadsheet with only the included cells
  • Select Clone
  • Rename the new spreadsheet ANOVA-1way_autosomal using the Clone Spreadsheet dialog
  • Select female_only from the Create new spreadsheet as a child spreadsheet: drop-down menu (Figure 5)
  • Select OK

Figure 5. Renaming and configuring filtered spreadsheet
  • Select () from the quick action bar to save the filtered spreadsheet
  • Specify a name for the spreadsheet, we chose autosomal, using the Save File dialog
  • Select Save to save the spreadsheet

It is best practice to occasionally save the project you are working on. Let's take the opportunity to do this now. 

  • Select File from the main command toolbar
  • Select Save Project...
  • Specify a name for the project, we chose Methylation, using the Save File dialog
  • Select Save to save the project

Saving the project saves the identity and child-parent relationships of all spreadsheets displayed in the spreadsheet tree. This allows us to open all relevant spreadsheets for our analysis by selecting the project file. 



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