[BioC] Limma-include interaction term

[James W. MacDonald]

Hi Jack,

On 6/12/2012 10:10 AM, Yao Chen wrote:
> Dear All,
>
> I try to find differential expressed genes between treat and untreated
> samples, and also I want to include the age effects.
>
> The design matrix is like this:
>
> treat  untreated  age
>    1        0            30
>    0         1           40
>    1        0            35
>
>
> The "treat" is factor, but "age" is continuous.  How can I set the
>   "cont.matrix"?

Pretty much just like you (or at least I) would expect:

contrast <- makeContrasts(treat - untreat, levels =  design)

But note that the design you are specifying allows different intercepts, 
but the slope is assumed to be the same for treated and untreated. If 
you want to allow different slopes as well, you need to introduce an 
age:treatment interaction term. Here I am assuming you have more than 
three samples.

Best,

Jim


>
> Thanks,
>
> Jack
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099