[BioC] desing matrix and interaction term difficulty

[James W. MacDonald]

Hi Brian,

A completely analogous example is in the limma User's Guide, section 
8.5.2.

Let us know if that doesn't answer your question.

Best,

Jim

On Friday, September 06, 2013 10:40:43 AM, Brian [guest] wrote:
>
> Dear Dr.Smyth and Limma users;
>
> Good morning.
> I have an experiment which has 4 variables; sham surgery, full surgery, treatment 1 and treatment 2. I am having difficulty formulating a design matrix and interaction terms for this experiment.  Treatment 1 is known to us and treatment 2 is the novel therapeutic.
>
> Groups are as follows:
> sham + treatment1
> sham + treatment2
> full + treatment1
> full + treatment2
>
> I need to answer:
> * gene exp difference between treat1 and treat2 in both models sham and full in order to verify full surgery working, and to prove treatment 2 is working to protect animal from full surgery detriments.  Treatment1 is considered a known drug with known effects.
>
> I am also confused (or ignorant) on how to employ a proper "difference of difference" or interaction term.
>
> I greatly appreciate any help and understand and respect everyone's time constraints.
> Thank you,
> Brian
>
>   -- output of sessionInfo():
>
> Q no code
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> 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