[BioC] LIMMA: question about design and contrasts

[James W. MacDonald]

Hi Patrick,

On 10/19/2012 1:10 AM, Patrick De Boever wrote:
> Dear all,
>
> We have used single color arrays for the following experiment:
>
> 25 individuals were split in 2 groups: location 1 and location 2. All individuals underwent an intervention.
> The individuals were analyzed twice: once before intervention and once after intervention.
>
> Which design should we use within LIMMA for assessing the effect of the location, the effect of the intervention, and possible interaction effect?

I think you will need to give more information. What do you mean exactly 
by '25 individuals were split in 2 groups: location 1 and location 2.' ?

That can be interpreted several ways. Are the locations sampling 
locations (e.g., one group was sampled from location 1 on their body, 
and the other was sampled from location 2) or are these physical 
locations (one group was recruited and samples were taken by lab 1 and 
the other group went to lab 2, and the two labs are in different parts 
of the country/university/world/whatever).

Best,

Jim


>
> Thank you for your kind reaction,
>
> Patrick
>
>
>
> Patrick De Boever, PhD, MSc
>
> Environment and Health Research                                  Centre for Environmental Sciences
> VITO NV                                                                                 Hasselt University - Campus Diepenbeek
> Industriezone Vlasmeer 7, 2400 Mol, Belgium              Agoralaan building D, 3590, Diepenbeek, Belgium
> Tel.   + 32 14 33 51 45                                                       patrick.deboever at uhasselt.be
> Fax.  + 32 14 58 05 23
> patrick.deboever at vito.be
>
> Visit our website: www.vito.be/english
>
>
>
> Sent from my iPad
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099