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
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.