hierarchical clustering with gene expression matrix in python

Posted by user248237 on Stack Overflow See other posts from Stack Overflow or by user248237
Published on 2010-06-04T22:51:04Z Indexed on 2010/06/05 16:02 UTC
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how can I do a hierarchical clustering (in this case for gene expression data) in Python in a way that shows the matrix of gene expression values along with the dendrogram? What I mean is like the example here:

http://www.mathworks.cn/access/helpdesk/help/toolbox/bioinfo/ug/a1060813239b1.html

shown after bullet point 6 (Figure 1), where the dendrogram is plotted to the left of the gene expression matrix, where the rows have been reordered to reflect the clustering.

How can I do this in Python using numpy/scipy or other tools? Also, is it computationally practical to do this with a matrix of about 11,000 genes, using euclidean distance as a metric?

thanks.

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