[BioC] Experimental Design

[Khan, Sohail]

Dear list,

I have the following samples:

wt-1        mut-1
wt-2	  mut-2
wt-3	  mut-3
wt-4        mut-4

The wt and the mut come from different plants. Question is, which is a better design??
To pool all the wt and used that as a common reference or use a loop design as follows.
cy3	cy5
wt-1	mut-1
mut-1	wt-2
wt-2	mut-2
mut-2	wt-3
wt-3	mut-3
mut-3	wt-4
wt-4	mut-4
mut-4	wt-1
In addition, which Bioconductor package can be used the analysis of the loop design?  Thank you for any suggestions.




Sohail Khan
Scientific Programmer
COLD SPRING HARBOR LABORATORY
Genome Research Center
500 Sunnyside Boulevard
Woodbury, NY 11797
(516)422-4076