Hi everyone:

I have one microarray data set considering differentiation in a cell line. About 7 time points for both control and treatment, no replicates
I would like to use limma to find the differentially expressed genes between time points for control and treatment, and want to compare the gene expression between control and treatment for the same time point. But I don't know how to make the right design and contrast matrix. 

After searching mail archive, the closest related answer is "https://stat.ethz.ch/pipermail/bioconductor/2010-June/033849.html", which suggest:

"
time=1:10
design=model.matrix(~time)
"

In my case, is it correct to set this?

time=rep(1:7,2)
design=model.matrix(~time)

> design
   (Intercept) time
1            1    1
2            1    2
3            1    3
4            1    4
5            1    5
6            1    6
7            1    7
8            1    1
9            1    2
10           1    3
11           1    4
12           1    5
13           1    6
14           1    7
attr(,"assign")
[1] 0 1


Then how to set the contrast matrix?


Thanks!

--
xuan



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