3.10. Building a gene tree

Click the Analysis>Clustering>Build gene tree command to open the "Tree calculation setup" dialog box from where you can define the parameters for building a gene tree for the current table.


Figure 3.10.1 "Tree calculation setup" dialog box.
1. The "Fields" button that calls the "Field selection" dialog box. 2. List of correlation coefficients. 3. The "Create expr. image" checkbox that creates an expression matrix map. 4. The "Make tree for fields" checkbox that determines the order of experiments by the tree of fields. 5. List of distance types. 6. List of amalgamation rules. 7. The "OK" button that starts building a tree. 8. The "Cancel" button the cancels building a tree.

3.10.1. The "Fields..." button opens the "Field selection" dialog box (see section 3.3). At the right of this button, you can see the number of selected fields.

3.10.2. The "Correlation type" list contains the following three correlation coefficients:

3.10.3. The "Distance type" list includes three types of distance measures calculated from the Rij correlation coefficients:

3.10.4. The "Amalgamation rule" list has four types of tree node combination:

3.10.5. The "Create expr. Image" checkbox. When this checkbox is checked, the program creates an expression matrix profile after it completes calculations.

3.10.6. The "Make tree for fields" checkbox. When this checkbox is checked, a similarity tree for the experimental values of the expression matrix is constructed, and the order of the experiments is determined by the field tree.

3.10.9. Control buttons:

Note. If no fields were selected, the "Error" information box will appear on your screen (Fig. 3.10.2). When the calculation is in progress, you will see the "Please wait" information box (Fig. 3.10.3). This information box will disappear after the calculation is complete.


Figure 3.10.2 "Error" information box.


Figure 3.10.3 "Please wait" information box.