The significant CpG loci detected in the previous step actually form a methylation signature that differentiates , which we shall now visualise by between LCLs and B cells. We can build and visualize this methylation signature using clustering and a heat map.

• Select the LCLs vs. B cells spreadsheet in the spreadsheet pane on the left
• Select Cluster Based on Significant Genes from the Visualization panel of the Illumina BeadArray Methylation workflow
• Select Hierarchical Clustering for Specify Method (Figure 1)
  
  

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• Select OK
• Verify that LCLs vs . B cells is selected in the drop-down menu
• Select Standardize for Expression normalization (Figure 2)
  
  

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SubtitleText Selecting spreadsheet and normalization method for clustering AnchorName Selecting normalization for clustering
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• Select OK 

The heat map will be displayed on the Hierarchical Clustering tab (Figure 3).

 

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SubtitleText Hierarchical clustering with heat map invoked on a list of significant CpG loci AnchorName heat map
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The experimental groups are rows, while the CpG loci from the LCLs vs . B cells spreadsheet are columns. Methylation levels are compared between the LCLs and B cells groups. CpG loci with higher methylation are colored red, CpG loci with lower methylation are colored green. LCLs samples are colored orange and B cells samples are colored red in the dendrogram on the the left-hand side of the heat map. 

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