The significant CpG loci detected in the previous step actually form a methylation signature, which we shall now visualise by a heat map. Start by selecting the shPOU5F1_vsPrimed

Select the list (CpG Loci of Interest) spreadsheet in the spreadsheet pane on the left and then invoking

Select Cluster Based on Significant Genes from the workflow. In the next dialog select Hierarchical Clustering and then use the Standardise as the normalisation procedure. If you are working on β-values, you may want to try out None, as well, since the distribution of β-values is confined to the interval between 0 and 1. Visualization panel of the Illumina BeadArray Methylation workflow

Select Hierarchical Clustering for Specify Method 

Select OK

Verify that 1/list (CpG Loci of Interest) is selected in the drop-down menu

Select Standardize for Expression normalization 

Select OK 

The heat map will be displayed on the Hierarchical Clustering tab (Figure 1).