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

Question

[Dipro]

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

[WouterDeCoster]

Hello Dipro!

It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/98425/ (and answered there)

This is typically not recommended as it runs the risk of annoying people in both communities.