[BioC] Re: experiment-design-advice-request (vijayaraj nagarajan)

[Christopher Wilkinson]

Hi vijay

I'm guessing that what you really want to know, is which genes have a different
response to treatement (ie the change in strain A after treatment with P is
different to the change in strain B after treatment with P).

If so I think design 1 is preferable, set up as a 2x2 factorial model which you
can easily setup and analyse with Limma. Design 2 is really just design 1 with
no AP-BP, and I don't think will estimate what you want as well as design 1.

Design 1 allows you to optimally estimate:
the (baseline) difference between strain A and B (alpha=BS-AS),
the difference between Peptide and Saline in stain A (beta=AP-AS),
which genes have different response to treatement (this is interaction of alpha
beta=(BP-BS) - (AP-AS)).

Its probably worth having a look at the following paper to understand how
different designs perform:
Glonek GF, Solomon PJ. 	Factorial and time course designs for cDNA microarray
experiments.Biostatistics. 2004 Jan;5(1):89-111.
PMID: 14744830 (or go to our website for a preprint)
Also check out the excellent limma users guide.

Cheers
Chris
>
> 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
>
Dr Chris Wilkinson

Senior Research Officer (Bioinformatics) | ARC Research Associate
Child Health Research Institute (CHRI)   | Microarray Analysis Group
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Christopher.Wilkinson at adelaide.edu.au

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