Gene lists can be visualized and their ability to distinguish samples evaluated using a hierarchical clustering heat map. Because of the batch effect in this data set, we will perform hierarchical clustering using batch-corrected intensity values. To do this, we need to open the fourtreatments list of differentially expressed genes as a child spreadsheet of the batch-remove spreadsheet
Select fourtreatments from the spreadsheet tree
Select () to close the spreadsheet
Select 1-removeresult (batch-remove) from the spreadsheet tree
Select File from the main tool bar
Select Open as child...
Select fourtreatments using the file browser
The fourtreatments spreadsheet will open as a child spreadsheet of batch-remove (Figure 1).
Figure 1. The fourtreatments spreadsheet is open as a child spreadsheet of bath-remove. Visualizations performed using fourtreatments will pull intensity values from batch-remove.
Visualizations performed using the fourtreatments spreadsheet will now use intensity values from the batch-remove spreadsheet.
To invoke hierarchical clustering, follow the steps below.
Select Cluster Based on Significant Genes from the Visualization section of the Gene Expression workflow
Select Hierarchical Clustering
Select OK
Select 1-removeresult/1 (fourtreatments) from the drop-down menu
Select Standardize for Expression normalization (Figure 2)
Figure 2. Configuring the Cluster the significant genes dialog
Select OK
The hiearchical clustering heat map will open in a new tab (Figure 3).
Figure 3. Hierarchical clustering of genes with significantly different expression across the treatment groups
Genes without changes in expression are given a value of zero and are colored black. Up-regulated genes have positive values and are displayed in red. Down-regulated genes have negative values and are displayed in green. Each sample is represented in a row while genes are represented as columns. Dendrograms illustrate clustering of samples and genes. To learn more about configuring the hierarchical clustering heat map, see the Hierarchical Clustering Analysis user guide.
For detailed information about the methods used for clustering, refer to the Partek Manual Chapter 8: Hierarchical & Partitioning Clustering.
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