Question: DESeq2 likelihood ratio test (LRT) design
0
gravatar for ijvechetti
11 days ago by
ijvechetti0
ijvechetti0 wrote:

Hello all,

I was wondering if you guys could help me with the design of my experiment.

Sample Condition Exercise HC1 Healthy No HC2 Healthy No HC3 Healthy No CPC1 CP No CPC2 CP No CPC3 CP No HE1 Healthy Yes HE2 Healthy Yes HE3 Healthy Yes CPE1 CP Yes CPE2 CP Yes CPE3 CP Yes

To look at interactions my design was the following: Full: ~ Condition + Exercise + Condition:Exercise Reduced: ~Condition + Exercise

So, if I want to look at genes that have any difference in the condition, I would do: Full: ~ Condition + Exercise Reduced: ~ Exercise

So, if I want to look at genes that have any difference in the exercise, I would do: Full: ~ Condition + Exercise Reduced: ~ Condition

That would be the way to analyze this data set?

Thanks in advance

deseq2 • 69 views
ADD COMMENTlink modified 11 days ago • written 11 days ago by ijvechetti0
Answer: DESeq2 likelihood ratio test (LRT) design
1
gravatar for Michael Love
11 days ago by
Michael Love26k
United States
Michael Love26k wrote:

Yes that’s the correct interpretation. Note we have a section on LRT in the vignette with some description.

ADD COMMENTlink written 11 days ago by Michael Love26k

Following up on that: -How would be the best design to look at the differences within the exercise but considering the condition?

Any suggestions would be much appreciated.

ADD REPLYlink written 7 days ago by ijvechetti0

I'd recommend meeting with a statistician to further understand how various designs work. My time on the support site is really designed for software support, not statistical analysis or experimental design consultation.

ADD REPLYlink written 7 days ago by Michael Love26k
Answer: DESeq2 likelihood ratio test (LRT) design
0
gravatar for ijvechetti
11 days ago by
ijvechetti0
ijvechetti0 wrote:

Thanks Michael. I just wanted to double-check

ADD COMMENTlink modified 7 days ago • written 11 days ago by ijvechetti0
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