Question: Doubt about batch effect and gene expression analysis
0
gravatar for Picasa
3.1 years ago by
Picasa590
Picasa590 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.

batch limma gene expression • 1.7k views
ADD COMMENTlink modified 3.1 years ago by Kevin Blighe71k • written 3.1 years ago by Picasa590
0
gravatar for Kevin Blighe
3.1 years ago by
Kevin Blighe71k
Republic of Ireland
Kevin Blighe71k wrote:

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

ADD COMMENTlink written 3.1 years ago by Kevin Blighe71k
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