Question: Doubt about batch effect and gene expression analysis
0
gravatar for Picasa
15 months ago by
Picasa390
Picasa390 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 • 692 views
ADD COMMENTlink modified 15 months ago by Kevin Blighe41k • written 15 months ago by Picasa390
0
gravatar for Kevin Blighe
15 months ago by
Kevin Blighe41k
Guy's Hospital, London
Kevin Blighe41k 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 15 months ago by Kevin Blighe41k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 897 users visited in the last hour