Dear all,


I have 32 transcriptomics profile of A. thaliana (single color), among
which15 received a drug treatment and 15 are the control group. For all
these samples, 2 biological observations were also obtained :
- life time of the plant (short or long)
- expression of an integrine (with or without)

I would like to get the following contrast :
(short life time without integrine) versus (long life time with integrine)
into treated samples
versus
(short life time without integrine) versus (long life time with integrine)
into control samples


I've set up my design matrix (target is below):

drug = as.factor(targetATH$drug)

integr  = as.factor(targetATH$integrin)

lifetime = as.factor(targetATH$lifetime)

design = model.matrix(~drug+integr+lifetime)

I can't figure out how to set up the correct contrast matrix to get the
coefficient I want.
I would be very grateful if you could give any pieces of advices for that.
I hope I have enough sample to get enough power to detect some genes.


many thanks by advance, best regards,
--
Dave


 target :
> targetATH
       FileName drug lifetime integrin
1   sample1.cel    Y        S        +
2   sample2.cel    Y        S        +
3   sample3.cel    Y        S        +
4   sample4.cel    Y        S        +
5   sample5.cel    Y        L        +
6   sample6.cel    Y        L        +
7   sample7.cel    Y        L        +
8   sample8.cel    Y        L        +
9   sample9.cel    Y        S        -
10 sample10.cel    Y        S        -
11 sample11.cel    Y        S        -
12 sample12.cel    Y        S        -
13 sample13.cel    Y        L        -
14 sample14.cel    Y        L        -
15 sample15.cel    Y        L        -
16 sample16.cel    Y        L        -
17 sample17.cel    N        S        +
18 sample18.cel    N        S        +
19 sample19.cel    N        S        +
20 sample20.cel    N        S        +
21 sample21.cel    N        L        +
22 sample22.cel    N        L        +
23 sample23.cel    N        L        +
24 sample24.cel    N        L        +
25 sample25.cel    N        S        -
26 sample26.cel    N        S        -
27 sample27.cel    N        S        -
28 sample28.cel    N        S        -
29 sample29.cel    N        L        -
30 sample30.cel    N        L        -
31 sample31.cel    N        L        -
32 sample32.cel    N        L        -

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