[BioC] Proper pooling design

[YUK FAI LEUNG]

Hi there,

I am designing a pilot microarray study on embryoic developmental mutant 
using affy platform. The comparison itself is very simple, the mutant vs 
normal at one time point. Due to various reasons (mostly funding and 
limited amount of tissue), I can't start with the "ideal" approach in 
which each sample is hybridized to an individual chip.

Since I can easily rear a lot of animals, it seems that pooling is the 
only choice for the pilot study. However I am not sure what is the best 
way to allocate the pooled samples to each chip. For example if I want 
to do 3 array replicates each for the mutant and control. Is it better 
to pool enough samples for 3 arrays and then separate the pooled sample 
in 3 portions for hybridization or just pool different individual 
samples for different replicates?

It seems to me that the first way is like getting a group expression 
average with accessment of technical variation, while the second 
approach can also provide some sort of evalution of biological 
variation, abeit an averaged one by the pooling. I suspect the latter 
approach is better, and would love to know the suggestions from you.

Thanks!

Fai

-- 
Yuk Fai Leung
Department of Molecular and Cellular Biology
Harvard University
BL 2079, 16 Divinity Avenue
Cambridge, MA 02138
Tel: 617-495-2599
Fax: 617-496-3321
email: yfleung at mcb.harvard.edu; yfleung at genomicshome.com
URL: http://genomicshome.com