Dear DESeq2 experts,
I have RNA-Seq data replicated from different genotypes. Let's say for the sake of example
sample genotype
samp1 A
samp2 A
samp3 B
samp4 B
samp5 C
samp6 C
samp7 D
samp8 D
and so on. I can easily compare each genotype against each other. Now let's say these genotypes have interesting common phenotypes (A and B have phenotype 1 and C and D have phenotype 2) and I want to compare combination of genotypes to find DEG that could explain the phenotypes. After reading DESeq2 vignette, manual, and several posts here and elsewhere, the only way I could think of to achieve this would be to write my condition file as :
sample phenotype
samp1 1
samp2 1
samp3 1
samp4 1
samp5 2
samp6 2
samp7 2
samp8 2
then run the results function with contrast 2 versus 1. Can someone confirm this is the right and only way of doing it or am I missing something obvious here?
Thanks for your answer. I looked into this way and I used to do something like this by the past:
res = results(dds, contrast = list(c("genotypeD", "genotypeC"), c("genotypeB","genotypeA")))
Only problem is that now it does not work because resultsNames() returns "genotype_D_vs_A", "genotype_C_vs_A" and so on and that's the only names DESeq2 accept with a list as value for the contrast argument
Hi Denis
Have you managed to find a solution? I just ran in the exact same problem and I was wondering if you found a way to overcome this limitation
EDIT: Well minutes after writing this I found the following link where they give a working solution
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