[Biopython] How to use Bio.Cluster

[Hongbo Zhu]

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