Question: Doubt about batch effect and gene expression analysis
0
Picasa • 560 wrote:
Hello,
I am looking for classical gene expression analysis between 2 conditions with the package limma.
The problem is that the samples have not been sequenced at the same time so I want to introduce a batch effect.
This is my model:
design <- model.matrix(~Batch + Condition, data = samples)
Intercept Batchb Batchc Batchd Condition
1 1 0 0 0 0
2 1 0 0 0 0
3 1 1 0 0 0
4 1 1 0 0 0
5 1 1 0 0 1
6 1 1 0 0 1
7 1 1 0 0 1
8 1 0 1 0 0
9 1 0 1 0 0
10 1 0 0 1 1
11 1 0 0 1 1
12 1 0 0 1 1
To analyse genes that are differentially expressed between condition 1 and 2 :
contr.matrix <- makeContrasts(Condition, levels = design)
Is it right, what I am doing ?. I am not sure whether I have to add something more in makeContrasts function.
Thanks for your help.
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modified 2.7 years ago
by
Kevin Blighe ♦ 65k
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written
2.7 years ago by
Picasa • 560
