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 form from the X and Y chromosomes, we first need to annotate the ANOVA spreadsheet with chromosome locations.

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• 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

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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. 

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• Select Clone
• Rename the new spreadsheet ANOVA-1way_Autosomal_Only autosomal using the Clone Spreadsheet dialog
• Select 1(Differential Methylation Analysis)Select female_only from the Create new spreadsheet as a child spreadsheet: drop-down menu (Figure 5)
• Select OK

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• Select () from the quick action bar to save the filtered spreadsheet
• Specify a name for the spreadsheet, we chose ANOVA-1way_autosomal_only, using the Save File dialog
• Select Save to save the spreadsheet

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

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