Hello, how do I calculate the correlation column of a GTR file?
Thanks
Hello, how do I calculate the correlation column of a GTR file?
Thanks
Dear Elizabetha,
The easiest way is to use a clustering tool such as cluster 3.0:
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm
there are also c and python implementations of clustering, and you can roll your own if you are familiar with math and programming.
Hi Alokito, I 've done my own application and now I want to show the clustering results in Java TreeView, that's why I need to generate the .gtr file. I calculate the last column as (1 - (distance between clusters / max distance between clusters)) but I'm not getting a pretty tree. Do you know if it is the right way to calcute the correlation needed?
Thanks in advance.
Traditionally, correlation values are calculated using the pearson correlation,
http://en.wikipedia.org/wiki/Correlation_and_dependence
which may or may not be applicable in your case. What do mean by "not pretty"? Do you have an example data file?
Yes, I have an example. How can I send it to you?
sure, could you submit it as a file attachment to a support request?
Log in to post a comment.