Question

Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis

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Dipro • 0

@dipro-13570

Last seen 7.0 years ago

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

deseq2 random effects batch effects RNA-seq rna-seq • 1.5k views

ADD COMMENT • link updated 7.4 years ago by Michael Love 43k • written 7.4 years ago by Dipro • 0

score 0 · Answer 1 · 2017-07-24

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Entering edit mode

Michael Love 43k

@mikelove

Last seen 6 days ago

United States

You can use ~batch + estrus + condition. This will correct for shifts in log counts due to batch and estrus.