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) 
  
  

• Select the Add as categorical option
• Select CHR (Figure 2)
  
  

• 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 X and Y chromosome columns to filter them out (Figure 3)
  
  

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)
  
  

• 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
  
  

• 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.