Thanks, James

How to include "age:treatment" interaction in the design matrix?

Jack

2012/6/12 James W. MacDonald <jmacdon@uw.edu>

> 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
>>
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>>
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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
>
>

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