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

Select the (LCLs vs. B cells) 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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SubtitleText	Selecting Heirarchical Clustering for clustering method
AnchorName	Selecting clustering method

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

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SubtitleText	Hierarchical clustering with heat map invoked on a list of significant CpG loci
AnchorName	heat map

The experimental groups are rows, while the CpG loci from the (LCLs vs. B cells) 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. B cells LCLs samples are colored red and LCLs orange and B cells samples are colored orange in red in the dendrogram on the the left-hand side of the heat map.

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