Question: EdgeR: Accounting for batch effects in a pairwise analysis
0
gravatar for cinderelliedoll
4.9 years ago by
United States
cinderelliedoll0 wrote:

Hello, 

I am wondering what the correct way to define the design in the EdgeR workflow is for a pairwise analysis, while also accounting for batch effects, in terms of the design <- model.matrix(~x+y) term. 

The setup of our experiment is quite simple: we have 18 cases who had blood RNA-seq before and after treatment, but these samples were run in different batches. Therefore, we expect batch effects and would like to correct for them. We would like to find the main effect of treatment without the effects of batch. 

Any help would be greatly appreciated. 

Thank you!

Anna

batcheffect paired • 953 views
ADD COMMENTlink modified 4.9 years ago by Gordon Smyth39k • written 4.9 years ago by cinderelliedoll0
Answer: EdgeR: Accounting for batch effects in a pairwise analysis
2
gravatar for Gordon Smyth
4.9 years ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:

Paired analyses are automatically batch corrected, because you are already correcting for the baseline level of each case. This serves to adjust for batch effects and indeed for any other differences between the cases. There no need to do anything extra in the analysis.

ADD COMMENTlink modified 3.8 years ago • written 4.9 years ago by Gordon Smyth39k
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 16.09
Traffic: 271 users visited in the last hour