[BioC] Experimental Design

Khan, Sohail khan at cshl.edu
Tue Jan 10 23:01:26 CET 2006

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
Genome Research Center
500 Sunnyside Boulevard
Woodbury, NY 11797

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