[Bioperl-l] Problem with clustering analysis of a large dataset (
18000 rows and 17 columns)
gongwuming at hotmail.com
Sat May 22 02:32:52 EDT 2004
Thanks for your reply.
I have done the same job under the MS Windows 2000 (using Eisen's original
cluster software for Windows) with the same computer (Pentium 4 2.4G with
512M memory) and the same method (avarage linkage clustering algorithm),
and the job was done in about 30 minutes, while the job failed under RedHat
9.0. Is the difference caused by the different OS or some other reasons?
I have another question about MCL. Could this method be used for gene
expression dataset not only for clustering proteins ?
College of Life Science, Wuhan University, China
>From: Andreas Kahari <ak at ebi.ac.uk>
>To: Gong Wuming <gongwuming at hotmail.com>
>CC: bioperl-l at bioperl.org
>Subject: Re: [Bioperl-l] Problem with clustering analysis of a large
dataset ( 18000 rows and 17 columns)
>Date: Fri, 21 May 2004 13:02:01 +0100
>As Aaron said, it's probably just waiting for disk.
>I'm not sure this helps you, but you could buy more memory or
>investigate other clustering approaches.
>MCL is fast:
>There is a package of it for Debian, and I've made a port of it
>to OpenBSD. Other unices should be able to compile it fairly
>easily out of the box. I've run larger sets than yours much
>quicker with the same memory size.
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