DESeq2 design model/contrasts question 3 level condition
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L_K • 0
@l_k-14850
Last seen 23 months ago

Hi everyone,

I am struggling with the implementation of the design model in DESeq2 for the following experiment:

Basically I have a condition factor with three levels: Control, Asymptomatic, Symptomatic.

It is clear how I'll perform the simple analysis for differentially expressed genes between asymptomatics and controls as well as between symptomatics vs controls separately.

However I am not sure how I should implement the comparison between symptomatic individuals versus asymptomatic individuals.

Would I have to do something like (Symptomatics - controls) - (Asymptomatics - controls)? And if yes, how would I implement that in DESeq2?

I would really appreciate anyone's help!

Thank you very much in advance!

-Matt

Edit:

I just found the following threads in this forum:

Use interactions to get the difference in the effect of two treatments

Should I contrast 2 treatment groups using the control group as reference or directly against each other?

And as I now realised I can simply do the tilde condition design with three levels and then do

results(dds, contrast=c("condition","symptomatic","asymptomatic"))

Sorry for not checking the existing threads not more thoroughly before posting.

 

deseq2 model design differential gene expression experimental design • 1.8k views
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@mikelove
Last seen 3 days ago
United States

I see you've answered your own Q. Just posting here to close the thread.

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