[BioC] Experimental Design

[Naomi Altman]

The best design depends on which comparisons are of most interest to you.

If you have 2 genotypes (wt and mutant) with 4 replicates of each and 
your objective is to compare wt to mutant, you are probably fine with 
a dye-swap design with 4 arrays, 1 wt and 1 mut on each array.

If the mutants are all different genotypes, then you need to 
replicate the mutants.  (In my opinion, this should be a separate set 
of plants - or at least a separate RNA extraction).  The best design 
depends on which comparisons are of most interest - comparisons among 
the mutants, or comparisons of each mutant to wt.  I cannot think of 
a situation in which I would want to use the loop design you have 
indicated below.

The main principle to remember is that the comparisons with most 
power are the 2 samples on the same array.

--Naomi



At 05:01 PM 1/10/2006, Khan, Sohail wrote:
>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
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111