Hi Guys,

thanks for confirmation. :-)

I was pretty sure because I have a little modified script of heatmap.2() where I added some features such as scaling "before" clustering where I can choose between z-score or just median centering, or having the signal color legend below or beside the heatmap ... stuff like that. In fact it even has a little module which I snatched from the HeatPlus package (I remember it was called like that) that should provide the possibility to color the dendrogram-clusters according to a given parameter defining either number of clusters of cut-heigt.

If somebody is interested just send me a notification. However I must warn you, that the modified code still has some minor bugs and is far from "package" ready, because I used to code it beside my projects and never had the time to concentrate on giving it a really final shape.

cheers

Benjamin


Am 22.07.2010 um 23:00 schrieb Sean Davis:

> 
> 
> 2010/7/22 Elmer Fernández <elmerfer@gmail.com>
> Hy Benjamin
> Are you sure about that? If so, I think that it is not correct, right?
> best
> Elmer
> 
> Hi, Elmer.  My reading of the source code for heatmap.2 suggests that Benjamin is correct.
> 
> Sean
>  
> 
> 2010/7/22 Benjamin Otto <b.otto@uke.uni-hamburg.de>
> 
> > 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@stat.math.ethz.ch [
> > bioconductor-bounces@stat.math.ethz.ch] on behalf of Sean Davis [
> > sdavis2@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@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
> > >>
> > >>       [[alternative HTML version deleted]]
> > >>
> > >>
> > >> _______________________________________________
> > >> Bioconductor mailing list
> > >> Bioconductor@stat.math.ethz.ch
> > >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> > >> Search the archives:
> > >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> > >>
> > >
> > >        [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor@stat.math.ethz.ch
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> > >
> >
> > ___________________________________________
> > 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
> > ___________________________________________
> >
> >
> >
> >
> >
> > --
> > Pflichtangaben gemäß Gesetz über elektronische Handelsregister und
> > Genossenschaftsregister sowie das Unternehmensregister (EHUG):
> >
> > Universitätsklinikum Hamburg-Eppendorf
> > Körperschaft des öffentlichen Rechts
> > Gerichtsstand: Hamburg
> >
> > Vorstandsmitglieder:
> > Prof. Dr. Jörg F. Debatin (Vorsitzender)
> > Dr. Alexander Kirstein
> > Joachim Prölß
> > Prof. Dr. Dr. Uwe Koch-Gromus
> >
> 
> 
> 
> --
> 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
> 
>        [[alternative HTML version deleted]]
> 
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 

___________________________________________
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
___________________________________________





-- 
Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG):

Universitätsklinikum Hamburg-Eppendorf
Körperschaft des öffentlichen Rechts
Gerichtsstand: Hamburg

Vorstandsmitglieder:
Prof. Dr. Jörg F. Debatin (Vorsitzender)
Dr. Alexander Kirstein
Joachim Prölß
Prof. Dr. Dr. Uwe Koch-Gromus

	[[alternative HTML version deleted]]

