C similarity matrix – Bio-Rad Quantity One 1-D Analysis Software User Manual
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Chapter 10. Reports
10-19
dendrogram will be recalculated. To return to the original tree, click on Restore
Original Tree.
The Min. and Max. sliders are active only for proportionally aligned Neighbor
Joining trees. Use them to adjust the minimum and maximum distances between
nodes on branches to highlight specific regions of data. Distances below the Min. or
above the Max. values will be collapsed to fit in the window.
For non-Neighbor Joining trees, use the Clusters option to define the number of
clusters (0 to 18) in the tree. The separate clusters will be identified in the tree by
letters.
10.5.c Similarity Matrix
The Similarity Matrix report compares the similarity of all the lanes to one another.
If there are N lanes in the gel, then the similarity matrix is an N by N matrix that is
computed using the Dice Coefficient as described in section 10.4, 1-D Analysis
Report.
The matrix has the following properties:
•
The diagonal elements always have values of 100. This is because a lane is
always 100 percent similar to itself.
•
The matrix is symmetrical (Mij = Mji).
Select Similarity Matrix from the Reports menu to open this report.