[BioC] AffyPLM's MAplot and cex

Ben Bolstad bmb at bmbolstad.com
Wed Mar 17 15:30:38 CET 2010

By setting the cex so small you have essentially thinned the number of
points that you are going to see. You could see the same effect 

x <- rnorm(100000)
y <- rnorm(100000)

Why that happens is not really specific to the MAplot() command.

Now you could also try something like


which may or may not acheive the effect you desired. Ypu can also use
cex.main to control the size of the title. eg


On Wed, 2010-03-17 at 13:52 +0800, Timothy Wu wrote:
> Hello,
> Caveat, I'm pretty new to R.
> I'm trying AffyPLM's MAplot by following example from "Quality Assessment of
> Affymetrix GeneChip Data" by Bolstad, et al. (
> http://www.springerlink.com/content/x88745lrpk331352/?p=5fe6247210644778b597610f5a5c6b43&pi=2)
> On page 36 when I made a call to MAplot(data, cex = 0.75). I tried changing
> the cex parameter to a small value (0.1), it appeared that not only text are
> made smaller, plots were also made smaller without corresponding change in
> coordinates. What I mean is a dot on a MA plot is changed in position in
> respect to the coordinates. This was not what I was expecting. My intention
> is only to change the size of the text "Median", "IQR" as well as the title.
> Was this normal?
> Timothy
> 	[[alternative HTML version deleted]]
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