Scatterplot Showing All Points

Yes, I agree.  (As an aside, there's actually a capital S in 
smoothScatter(), and it's a bit of a pain to install, because 
geneplotter depends on something that depends on DBI, which is not so 
easily available these days.)

Somehow I always forget the capital S and wonder if I have loaded the 
correct package ;-D

As for installing the required dependencies, I believe this is actually 
quite straightforward:

source("http://www.bioconductor.org/biocLite.R")
biocLite("geneplotter")

Should install geneplotter and all required dependencies.

Best,

Jim

Duncan Murdoch

James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623