Hi!
So I'm basically asking the same question as [this post][1], but have a slightly more complex design and want to make sure I'm setting up the proper contrasts.
I have samples from two different genotypes (B6 & TCR) reared in 3 stress conditions (no stress, NS; single hit, SH; double hit, DH). I am interested in the main effect of genotype, the main effect of stress, and the interaction between the two and so have coded my design like so: ~ genotype+ DoubleHit+ Genotype:DoubleHit.
I understand that retrieving results as follows:
res = results(dds, name = 'GENOTYPE_TCR_vs_B6')
only gives me the effect of genotype within the reference level of stress. I have already releveled the factor in the metadata such that no stress is the reference level.
I want the main effect of genotype independent of stress and vice versa.
I have resultsNames as follows:
[1] "Intercept" "GENOTYPE_TCR_vs_B6" "DoubleHit_SH_vs_NS"
[4] "DoubleHit_DH_vs_NS" "GENOTYPETCR.DoubleHitSH" "GENOTYPETCR.DoubleHitDH"
What is the correct way to set up contrasts in the results function to get the desired outcome?
My attempt at getting the main effect of genotype independent of stress:
res = results(dds, contrast=c(0,1,0,0,0.5,0.5))
And vice versa:
res = results(dds, contrast=c(0,0,1,1,0.5,0.5))
If I'm on track or way off base please let me know! Furthermore, how would setting the contrast to 1 for only one stress condition (ex. if I'm only interested in DH vs NS) compare to setting them both to one for interpretation?
Thanks so much in advance!
