How do I create clustering tree/view with a distance matrix?
Sep 28, 2012 4:35 PM(1790 views)
I am trying to visualize the organization of some data with JMP9.
I have N samples and I have calculated a distance matrix of N*N with my own formula. For example, I have shown some made up 4X4 comparison matrix here.
10012 10013 10014 10015
10012 0 100 100 200
10013 2 0 300 100
10014 300 100 0 33
10015 30 200 38 0
I opened this matrix in JMP. Then I tried to use the Analyze->Multivariant -> Cluster. Then I clicked the "Data is Distance Matrix" and clicked OK button. Then nothing happened. Exactly how do I do it? Anyone with any experience?
Hi - I've just tried it myself: it works for me in both JMP 9 and JMP 10. You'll need to load your data into a data table as five columns called (for example) "ColName", "10012", "10013", "10014" and "10015" respectively, with each column consisting of four rows, and ColName containing the four numbers 10012, 10013, 10014 and 10015 (because the column containing the identifiers needs to correspond to the names of the columns containing the actual data). Then just call up Analyze | Multivariate Methods | Cluster, click on "Data is distance matrix" as you've already described, and identify column "ColName" as the Label column in the resulting dialog screen. You should get a warning to the effect that your distance matrix isn't symmetric, but it will actually be analyzed.
I've tried entering the column identifiers as both numeric and alphabetic: it doesn't seem to make any difference.