[R] plotDensity

[Henrik Bengtsson]

There is no plotDensity() function in 'limma', but plotDensities().

FYI, there are 1000+ CRAN packages, several hundred Bioconductor
packages, and probably another 1000 packages elsewhere, so please be
precise in order to avoid confusion (and time waste).  Take a minute
or two to read the following:

> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html

The vertical scale for plotDensities() in limma gives you the density
at any position scaled such that integral (the area under the curve)
is one.  This is also true for plotDensity() in aroma.light
(Bioconductor), which explicitly says so in the vertical label.
They are both utilizing the density() function in the 'stats' package.
 See help(density) for more details.  Typically you don't interpret
the exact value at a particular position, but rather the relative area
under the curve for an interval of interest compared with another
interval of interest.

Hope this helps

Henrik


On Feb 19, 2008 7:23 AM, Conny Schmitt <laptopcss at gmx.de> wrote:
> Hallo,
>
> I just loaded the limma package.
>
> Conny
>
> -------- Original-Nachricht --------
> > Datum: Tue, 19 Feb 2008 06:41:18 -0800
> > Von: "Henrik Bengtsson" <hb at stat.berkeley.edu>
> > An: laptopcss at gmx.de
> > CC: r-help at stat.math.ethz.ch
> > Betreff: Re: [R] plotDensity
>
>
> > Is 'plotDensity' a specific function you are referring to?  If so, in
> > which package?  Then we can give a straight answer...
> >
> > /Henrik
> >
> > On Feb 19, 2008 4:10 AM,  <laptopcss at gmx.de> wrote:
> > > Hallo,
> > >
> > > I have a question to plotDensity and do not understand what stand
> > behind. In a density plot the x-axis is the signal intensity but for what stands
> > than density on the y-axis? Here I have the values 0.00-0.30 Can anyone
> > discribe it by his own words? I do not understand the help.
> > >
> > > Thanks, Conny
> > > --
> > >
> > > ______________________________________________
> > > R-help at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> > >
>
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