[BioC] Limma function plotDensities question

Jenny Drnevich drnevich at uiuc.edu
Wed Jul 26 16:43:58 CEST 2006

Hi Pete,

plotDensities() and most plotting functions will take the graphical 
parameters 'xlim=' and 'ylim='. In your case, you would do:

 > plotDensities(yourobject, xlim=c(-10,30))

I would be concerned about getting such apparently HUGE numbers in some 
cases after your normalization - especially because the default for 
plotDensities is to plot R & G values in log2 scale!  The extreme negative 
numbers in log2 are caused by very small positive numbers, but on the other 
end you shouldn't be getting anything close to 10000, or even 50 for that 
matter. It's probably only a few spots that are behaving strangely after 
the normalizations, but you might want to have a closer look at them.


At 08:17 AM 7/26/2006, Pete wrote:
>I'm still fairly new to all this so this may be a simple question. I have a
>problem sometimes when using the plotDensities function in Limma, in some
>cases the plot produced is on such a scale that the lines are not
>distinguishable. Usually the intensity axis is in the range of -10 :30,
>however ocassionally after a printtip lowes normalisation, or some
>betweenArrayNormalizations, the scale of the graph is -5000:10000 with the
>density peak being a single spike in the middle of the plot.  Is there a way
>to control the axis scale? or is there an easy way to set a minimum and
>maximums for an MA object?
>Many thanks
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Search the archives: 

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

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

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