[Bioperl-l] Problem with clustering analysis of a large dataset ( 18000 rows and 17 columns)

[Gong Wuming]

Hi.
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 ?

Sincerely

Wuming Gong
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:
>
>     http://www.micans.org/mcl/
>
>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.
>
>Cheers,
>Andreas
>

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