Doubt about batch effect and gene expression analysis

Question

[Picasa]

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.

Answer 1

[Kevin Blighe]

You may want to take a look at this thread on Bioconductor: https://support.bioconductor.org/p/66251/ Approach 2 appears to be the recommended one.

Kevin