[BioC] experiment-design-advice-request

[vijayaraj nagarajan]

hi anja, christopher and naomi
thanks a lot for those nice suggestions. 
i read that paper by Glonek and Solomon. that was really helpful.
thanks again
vijay


Anja Schiel <a.e.schiel at lumc.nl> wrote: 
Hi Vijay
I recommend reading an article from Glonek and Solomon (Biostatistics,
2004, 5,1,89:111). You will find good arguments for the loop design and
why certain comparisons are not as informative as others. Anyhow, there
are a lot of good articles about microarray design available.

Anja



On Sat, 2005-04-30 at 11:49 -0700, vijayaraj nagarajan wrote:
> hi friends
> we are designing a microarray experiment, where there are two different mouse strains (A,B)...
> and one condition (Peptide - P and Saline - S). we expect the mouse strains to express differentially even under normal (saline) conditions...so we did not want to go for pooling the controls, to have a common - pooled control... under this scenario...
> 
> which of the following designs would you suggest....(we have planned to use dyeswap and 2 replicates for each hybrisation)....
> 
> 1:
> 
> AP---BP
> | \ / |
> | / \ |
> AS---BS
> 
> (all pairs - with 6 hybridisations)
> OR
> 
> 2: 
> 
> AP
> |
> AS---BS
> |
> BP
> 
> (with just 3 hybridisations, so that we could deduce AP-BP,using AP-AS-BS and rest like that...)
> 
> i request your valuable advice in this regard....
> thanks 
> 
> vijay
> graduate student
> department of biological sciences
> University of Southern Mississippi
> MS
> 
> 
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-- 
Anja E. Schiel, Ph.D.
Departments of General Internal Medicine and Human Genetics
Leiden University Medical Center
PO Box 9503
2300 RA Leiden
The Netherlands 
tel: -31-(0)71-5276067
fax: -31-(0)71-5276075 



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