[BioC] the design matrix again

[HuW at mskcc.org]

Hi everyone, 

I know my question is answered in some extent on mail list. But I am still not feel very confidence about my design. I really appreciate if anyone can help me on this. 

the data set is about the patients before and after treatment. for example, for 3 patients. I want to find out the genes that changed expression before and after treatment. if I have 3 patients, I did like this:

>design
  patient1 patient2 patient3 treatment14
1        1        0        0           0
2        0        1        0           0
3        0        0        1           0
4        1        0        0           1
5        0        1        0           1
6        0        0        1           1
attr(,"assign")
[1] 1 1 1 2
attr(,"contrasts")
attr(,"contrasts")$patient
[1] "contr.treatment"

attr(,"contrasts")$treatment
[1] "contr.treatment"

>eset.rma.fit = lmFit(eset.rma, design);
>eset.rma.bayes = eBayes(eset.rma.fit);
>topTable(eset4.rma.bayes, coef = "treatment14", adjust = "BH");

thank you very much. 

Wenhuo Hu
 
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