[SciPy-User] Identifying variables driving divergence in Scipy

Ben Temperton btemperton@gmail....
Thu Dec 20 16:44:43 CST 2012


Hi there,

I have a matrix of 37 samples and ~1300 variables that are clearly 
clustering into 3 distinct groups using:

import scipy.cluster.hierarchy as sch
import scipy.spatial.distance as dist

d1= dist.pdist(mtx2, 'braycurtis')
Y1 = sch.linkage(d1, method='average', metric='braycurtis')
Z1 = sch.dendrogram(Y1, labels=mtx2.index)

What I would like to do is find out which variables are driving the 
divergence in this clustering, i.e. which ones are greater in group A than 
group B and vice versa. In tools like Primer, this would be done with a 
SIMPER test, and I am hoping someone can point me in the direction of a 
Scipy equivalent as I am trying to keep all my data analysis in ipython 
notebook.

Many thanks,

Ben



<https://lh5.googleusercontent.com/-YdYGFVthrYk/UNOUWRM4OsI/AAAAAAAAAkI/VBJvYtIbPJo/s1600/clust.png>

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