Hierarchical Clustering
The gene list in spreadsheet Down_Syndrome_vs_Normal (A) can be used for hierarchical clustering to visualize patterns in the data.
- Under the Visualization section in the Gene Expression workflow, select Cluster Based on Significant Genes (Figure 1)
- The Cluster Significant Genes dialog asks you to specify the type of clustering you want to perform. Select Hierarchical Clustering and select OK
- Choose the Down_Syndrome_vs_Normal (A) spreadsheet under the Spreadsheet with differentially expressed genes
- Choose the Standardize – shift genes to mean of zero and scale to standard deviation of one under the Expression normalization panel. This option will adjust all the gene intensities such that the mean is zero and the standard deviation is 1
- Select OK to generate a Hierarchical Clustering tab (Figure 2)
For more information on the methods used for clustering, you can refer to Chapter 8: Hierarchical & Partitioning Clustering in Help > User’s Manual. For a tutorial on configuring the clustering plot, please refer to the user guide that can be downloaded from: here or from Help >On-line Tutorials > User Guides.
Adding Gene Annotation
During data importation, the GeneChip annotation file was linked to the imported data. This linked annotation information can be added as new columns to the ANOVA or gene list spreadsheets. For example, we can add additional annotation to the gene list we created from the ANOVA results as follows:
- In the Down_Syndrome_vs_Normal (A) spreadsheet, right click on the second column header 2. ProbesetID and select Insert Annotation from the pop-up menu (Figure 3)
- Select Chromosomal Location under the Column Configuration panel (Figure 4). Leave everything else as default and select OK
- To create a dot plot showing expression levels of a specific gene for each sample, right click on the row header and select Dot Plot (Orig. Data) from the pop-up menu. This generates a Dot Plot tab for the selected gene (Figure 5)
Additional Assistance
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
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