[Biopython] How to use Bio.Cluster

Hongbo Zhu macrozhu at gmail.com
Tue Apr 19 19:04:20 UTC 2011


Hi, Ogan,

if it is just centering the data, can you calculate the mean or median and
do the centering by yourself? The cluster module has mean() and median()
functions.
http://biopython.org/DIST/docs/api/Bio.Cluster.cluster-module.html

regards,hongbo

On Tue, Apr 19, 2011 at 7:21 PM, Ogan ABAAN <oda.gumail at gmail.com> wrote:

> Hi all,
>
> I am trying to use Bio.Cluster and also comparing the output with the data
> generated by Cluster GUI. In the GUI version there is a tab "Adjust data"
> where you can center genes and center arrays for either mean or median.
> Doing that seems to give nice looking trees. However, Bio.Cluster do not
> seem to have the function to center data or I don't see it. So the trees are
> always black and red with no intermediate values. I tried scaling without
> any improvement.
>
> Does anybody know a why to achieve centering. I am using
> Bio.Cluster.treecluster.
>
> Thanks
>
> Ogan
>
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-- 
Hongbo



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