[BioC] Experimental Design
naomi at stat.psu.edu
Wed Jan 11 04:09:48 CET 2006
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
The main principle to remember is that the comparisons with most
power are the 2 samples on the same array.
At 05:01 PM 1/10/2006, Khan, Sohail wrote:
>I have the following samples:
>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.
>In addition, which Bioconductor package can be used the analysis of
>the loop design? Thank you for any suggestions.
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Naomi S. Altman 814-865-3791 (voice)
Dept. of Statistics 814-863-7114 (fax)
Penn State University 814-865-1348 (Statistics)
University Park, PA 16802-2111
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