Entering edit mode
4.8 years ago
ResearchR
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120
Dear all,
I am running a phylogenetic analysis (R-package 'ape') based on methylation data. The samples in my phylogenetic tree can be grouped in three class. Now I would like to test, if group 1 is more similar to group 2 or group 3. Using a bootstrap approach does not really do the job, since I would like to make a quantitative statement involving a computed statistic. Blomberg’s K or similar approaches (as far as I understood them) are not suited to answer my question. I would appreciate some help since phylogenetic analysis is not my field of expertise.
Thank you very much guys for your help.
Cheers!
Are you building the tree? Using what data? What is the organism?
More to the point, by "more similar to" I guess you mean have a common ancestor which is younger than the common ancestor of the other two groups. You can actually answer this question using the bootstrap.
I already built the tree based in methylation beta-values derived from humans. The bootstrap will create trees based on a random subset of the 'main' tree. Could you please tell me how I can see the common ancestor from that analysis? Btw, thanks for your comment!
Sorry but I still can't understand what the tree represents.
The tree represents the development of a tumor in comparison to control tissue. The control tissue is derived from two different locations. Now I would like to make a statement if location 1 or location 2 is most likely the ancestor of the tumor. Does this help?
Thanks for the explanation. If you already built the tree you should already have the answer. If you want confidence you can use bootstrapping and count the number of trees in which you get the same answer.
I think I figured it out! Thanks for your help!!!!