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

[Benjamin Otto]

Hi Guys,

do note that the scale() function in heatmap doesn't scale your values till AFTER clustering for visualization purpose! So if you provide already scaled data, you naturally will expect a different result.

cheers

Benjamin

Am 22.07.2010 um 16:25 schrieb 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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>> 
>> 
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> 
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___________________________________________
Benjamin Otto, PhD
University Medical Center Hamburg-Eppendorf
Institute For Clinical Chemistry / Central Laboratories
Campus Forschung N27
Martinistr. 52,
D-20246 Hamburg

Tel.: +49 40 7410 51908
Fax.: +49 40 7410 54971
___________________________________________





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