[BioC] [mArray] scale for spatial plots

[Sean Davis]

Francis

You just need to add a zlim parameter to your maImage call.  For example, if
the minimum expression is 20 (across foreground and background) and the max
expression is 10000 (again, across foreground and background), issuing the
commands:

maImage(christian.raw[,1],x="maGf",xlim=c(20,10000))

and 

maImage(christian.raw[,1],x="maGb",xlim=c(20,10000))

Will get you plots that have the same scale varying from 20 to 10000.

Sean
-- 
Sean Davis, M.D., Ph.D.

Clinical Fellow
National Institutes of Health
National Cancer Institute
National Human Genome Research Institute

Clinical Fellow, Johns Hopkins
Department of Pediatric Oncology
-- 




On 1/13/04 11:23 AM, "Foata,Francis,LAUSANNE,NRC/N&H"
<francis.foata at rdls.nestle.com> wrote:

> Hello,
> 
> I did some Spatial plot using the following R code:
> 
> maImage(christian.raw[,1], x="maGf") for green foreground
> or
> maImage(christian.raw[,1], x="maGb") for green backgound
> This works perfectly.
> 
> Now for diagnostic purposes I want to compare foreground to background
> intensities. The problem is that the intensity scale of the plot (indicated
> in each plot on the right where colour is correlated to intensity) is done
> automatically and of course varies between fore- and background.
> 
> Is there a way to adjust the scale manually?
> 
> Thanks,
> 
> Francis
> 
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> 
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