back to standardization discussion, is it better to do 
1- mean centering, or 
2- median centering of variables or 
3- mean = 0, standard deviation = 1 of variables?

1 and 2 could be done with scale function (center = T). so we would know what the results would be.

Jenny Drnevich <drnevich@uiuc.edu> wrote: Hi,

I prefer not to standardize around 0 or use the 
scale="row" option of heatmap2, because it's not 
always clear what the resulting values mean. What 
I've done is to add a row to the data to force the center to be on zero:

 > class(mean.sig.05)
[1] "matrix"

 > dim(mean.sig.05)
[1] 101  15

 > max(mean.sig.05)
[1] 3.24023

 > min(mean.sig.05)
[1] -3.120530

 > mean.sig.05 <- rbind(mean.sig.05,fake=c(3.24,rep(0,13),-3.24))

 > rownames(mean.sig.05) <- NULL

 >hmcol2 <- colorRampPalette(c("red","white","blue"))(256)

 > heatmap_2(mean.sig.05,col=hmcol2,legend=1,do.dendro=c(T,T),scale="none")

Of course, it's not ideal to have a faked row of 
data in the plot, but it doesn't really show if you have >50 genes.

Cheers,
Jenny

At 06:24 AM 8/1/2007, Benjamin Otto wrote:
>How about data standardization before plotting? Should center the values
>automatically around 0. There is some flag in the function to da that,
>but I don't have it in mind right now.
>
>regards,
>
>Benjamin
>
>
>Am Dienstag, den 31.07.2007, 09:56 +0200 schrieb Kauer Maximilian Otto:
> > Dear list,
> >
> > Is there a way to force the colors in 
> heatmap.2 to center on 0 i.e to to force 0 to 
> be white even though the spread in the data is 
> unequal (say -7 to +4)? I'm using bluered, but could use different color sets.
> >
> > Thank You,
> > Max
> >
> > _______________________________________________
> > 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
> >
>
>
>
>--
>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
>Ricarda Klein
>Prof. Dr. Dr. Uwe Koch-Gromus
>
>
>_______________________________________________
>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

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich@uiuc.edu

_______________________________________________
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

 

Jenny Drnevich <drnevich@uiuc.edu> wrote: Hi,

I prefer not to standardize around 0 or use the 
scale="row" option of heatmap2, because it's not 
always clear what the resulting values mean. What 
I've done is to add a row to the data to force the center to be on zero:

 > class(mean.sig.05)
[1] "matrix"

 > dim(mean.sig.05)
[1] 101  15

 > max(mean.sig.05)
[1] 3.24023

 > min(mean.sig.05)
[1] -3.120530

 > mean.sig.05 <- rbind(mean.sig.05,fake=c(3.24,rep(0,13),-3.24))

 > rownames(mean.sig.05) <- NULL

 >hmcol2 <- colorRampPalette(c("red","white","blue"))(256)

 > heatmap_2(mean.sig.05,col=hmcol2,legend=1,do.dendro=c(T,T),scale="none")

Of course, it's not ideal to have a faked row of 
data in the plot, but it doesn't really show if you have >50 genes.

Cheers,
Jenny

At 06:24 AM 8/1/2007, Benjamin Otto wrote:
>How about data standardization before plotting? Should center the values
>automatically around 0. There is some flag in the function to da that,
>but I don't have it in mind right now.
>
>regards,
>
>Benjamin
>
>
>Am Dienstag, den 31.07.2007, 09:56 +0200 schrieb Kauer Maximilian Otto:
> > Dear list,
> >
> > Is there a way to force the colors in 
> heatmap.2 to center on 0 i.e to to force 0 to 
> be white even though the spread in the data is 
> unequal (say -7 to +4)? I'm using bluered, but could use different color sets.
> >
> > Thank You,
> > Max
> >
> > _______________________________________________
> > 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
> >
>
>
>
>--
>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
>Ricarda Klein
>Prof. Dr. Dr. Uwe Koch-Gromus
>
>
>_______________________________________________
>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

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich@uiuc.edu

_______________________________________________
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


       
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