Question: design and contrast matrix for limma time series without replicates
0
Chunxuan Shao • 30 wrote:
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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modified 7.7 years ago
by
James W. MacDonald ♦ 52k
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written
7.7 years ago by
Chunxuan Shao • 30

