[BioC] Problems with heatmap on genes...

Johan Lindberg johanl at biotech.kth.se
Wed Nov 10 09:43:43 CET 2004

Hi Giulio. Heatmap is as you say a great tool if you have a small number
of genes but NOT if you have a lot of genes. I was dealing with the same
thing as you are doing now some 6 month ago and I found no good solution
using Heatmap. Therefore we use the freeware (note freeware) MeV from
TIGR at our department to do hierarchical clustering and similar things.


What we have done is to write a script (exportMEV) that takes an
MA-object (package Aroma in R) and export that object to MeV format and
use it when doing clustering.

Best regards

// Johan Lindberg

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Giulio Di
Sent: Tuesday, November 09, 2004 4:38 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Problems with heatmap on genes...


I'm trying to have a clear figure of gene clusters using heatmaps, but
more than 100-200 genes it's not possible to do it, with default options

(and I would like to do that with 1500 genes or so...). Gene names (and 
branchs too) collapse together...

I tried, setting new device dimensions (jpeg() or png() height and
and modifying par() options (fin, etc..), to have long cluster figures
be clear, dChip style). Well, it works for others high-level graphical 
functions, but it doesn't work for heatmaps().  I always obtain big
but with exactely the same squared heatmap inside.

I spent long time on the documentation and searching the web, and when I

found something, it was always some heatmaps for 50-100 genes at max

I trust that someone working on gene clustering is confidential on this,
and I will appreciate a lot any suggestion... I almost became crazy on

Thanks in advance,


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