Re: [R] plotDensity

From: Henrik Bengtsson <hb_at_stat.berkeley.edu>
Date: Tue, 19 Feb 2008 08:24:33 -0800

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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