Question: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
0
gravatar for Dipro
23 months ago by
Dipro0
Dipro0 wrote:

Hi,

I was wondering if I could get some advice on controlling for random effects using DESeq2. For example, given simulated data:

Treatment Batch Estrus
Control 1 1
Control 2 2
Control 3 1
Control 4 1
Control 1 2
Control 2 2
Control 3 2
Control 4 1
Control 1 3
Control 2 1
Treated 3 3
Treated 4 3
Treated 1 2
Treated 2 3
Treated 3 2
Treated 4 3
Treated 1 2
Treated 2 1
Treated 3 1
Treated 4 2

What is the best way to control for batch and estrus? I understand that DESeq2 does not support random effect analysis. As such, I was wondering if I could be advised on a work around for this type of analysis?

Thanks

ADD COMMENTlink modified 23 months ago by Michael Love23k • written 23 months ago by Dipro0
Answer: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
0
gravatar for Michael Love
23 months ago by
Michael Love23k
United States
Michael Love23k wrote:
You can use ~batch + estrus + condition. This will correct for shifts in log counts due to batch and estrus.
ADD COMMENTlink written 23 months ago by Michael Love23k

Thanks very much for your input Michael

ADD REPLYlink written 23 months ago by Dipro0
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