[BioC] AffyPLM's MAplot and cex

[Ben Bolstad]

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)
plot(x,y,pch=".")
plot(x,y,pch=".",cex=0.1)

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


Now you could also try something like

MAplot(Data,cex=0.1,pch=20)


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

MAplot(Data,cex.main=0.1)






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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