[BioC] Heatmap.2 scale problems: Sacling inside the function gives different results than scaling outside!!!

[Bazeley, Peter]

Hi Elmer,

The default scale option in heatmap.2 scales by row, whereas the scale() function scales by column, so this is probably why there is a difference. I think whichever dimension contains unique samples is how you want to scale (if this was expression data, for example).


Pete
________________________________________
From: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] on behalf of Sean Davis [sdavis2 at mail.nih.gov]
Sent: Thursday, July 22, 2010 9:17 AM
To: Elmer Fernández
Cc: Bioconductor mailing list
Subject: Re: [BioC] Heatmap.2 scale problems: Sacling inside the function       gives different results than scaling outside!!!

2010/7/22 Elmer Fernández <elmerfer at gmail.com>

> Dear Users
> I'm working with the heatmap.2 function and I realize that if you use the
> scale input paramenter gives different results than usign the scale
> function
> outsie and feed the heatmap.2 fucntion with the scaled matrix. I attached
> the results of the two approaches and the used data matrix (M.csv).
> SO, what I'm doing wrong?
>
>
Hi, Elmer.

The default distance function used by heatmap.2 is dist() which is not going
to be invariant under centering and scaling, I don't think.  It looks like
you are using that default.

Sean


> R Code
>
> library(gplots)
> M=matrix(c(rnorm(10*3,1,2),rnorm(10*2,-0.5,1)),ncol=5)
> heatmap.2(M,scale="column",trace="none",main="scaled inside")
> x11();heatmap.2(scale(M),scale="none",trace="none",main="scaled outside")
>
> > sessionInfo()
> R version 2.10.0 (2009-10-26)
> x86_64-unknown-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C
> LC_TIME=en_US.UTF-8           LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8       LC_MESSAGES=en_US.UTF-8
> LC_PAPER=en_US.UTF-8          LC_NAME=en_US.UTF-8
>  [9] LC_ADDRESS=en_US.UTF-8        LC_TELEPHONE=en_US.UTF-8
> LC_MEASUREMENT=en_US.UTF-8    LC_IDENTIFICATION=en_US.UTF-8
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] gplots_2.7.4   caTools_1.10   bitops_1.0-4.1 gdata_2.7.1
> gtools_2.6.1   rkward_0.5.1
>
> loaded via a namespace (and not attached):
> [1] tools_2.10.0
>
>
> --
> Elmer A. Fernández (Bioing. PhD)
> Investigador Asistente CONICET - Research Assistant CONICET
> Prof. Inteligencia Artificial -UCC - Prof. Artificial Intelligence @ UCC
> tel: +54-(0)351-4938000 int 145
> Fax: +54-(0)351-4938081
> web page : http://www.uccor.edu.ar/modelo.php?param=3.8.5.15
> http://sites.google.com/site/biologicaldatamininggroup/Home/
> mail address: Camino Alta Gracia Km 7.1/2- Córdoba-5017-Argentina
>
>
>
> --
> Elmer A. Fernández (Bioing. PhD)
> Investigador Asistente CONICET - Research Assistant CONICET
> Prof. Inteligencia Artificial -UCC - Prof. Artificial Intelligence @ UCC
> tel: +54-(0)351-4938000 int 145
> Fax: +54-(0)351-4938081
> web page : http://www.uccor.edu.ar/modelo.php?param=3.8.5.15
> http://sites.google.com/site/biologicaldatamininggroup/Home/
> mail address: Camino Alta Gracia Km 7.1/2- Córdoba-5017-Argentina
>
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