page 124 (Section 1.4.2): Analysis of microarray data:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The data that are shown in Plate 3 are included, and a simple form of
analysis demonstrated, in the DAAGbio package that is available from 
CRAN.

1) install the package DAAGbio from CRAN, also installing limma at 
the same time.  Then type in

vignette(package="DAAGbio")

This gives the name of the vignette that demonstrates the analysis.  

2) To display the vignette, type:

 vignette("marray-notes")

A better analysis would allow for a correlation between the spots 
on each pair of half-slides, for which limma does have the facility.
Consult the limma manual for details.

3) Type help.start() to open the documentation browser Window, then 
navigate

Packages | DAAGbio | directory

This navigates to the directory that holds the raw data and 
information files from which the data can be read in, as described
in the vignette.

John Maindonald
April 24, 2006.