problem with hierarchical clustering in Python

Posted by user248237 on Stack Overflow See other posts from Stack Overflow or by user248237
Published on 2010-05-30T22:52:41Z Indexed on 2010/05/30 23:02 UTC
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python

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numpy

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machine-learning

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scipy

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hcluster

I am doing a hierarchical clustering a 2 dimensional matrix by correlation distance metric (i.e. 1 - Pearson correlation). My code is the following (the data is in a variable called "data"):

from hcluster import *

Y = pdist(data, 'correlation')
cluster_type = 'average'
Z = linkage(Y, cluster_type)
dendrogram(Z)

The error I get is:

ValueError: Linkage 'Z' contains negative distances.

What causes this error? The matrix "data" that I use is simply:

[[  156.651968  2345.168618]
 [  158.089968  2032.840106]
 [  207.996413  2786.779081]
 [  151.885804  2286.70533 ]
 [  154.33665   1967.74431 ]
 [  150.060182  1931.991169]
 [  133.800787  1978.539644]
 [  112.743217  1478.903191]
 [  125.388905  1422.3247  ]]

I don't see how pdist could ever produce negative numbers when taking 1 - pearson correlation. Any ideas on this?

thank you.

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