DESeq2 result contrast

Question

[hamsasekar02]

I have three genotypes (I,II,III) and conditions (infected,mock)

When i do the DESeq2 analysis with model Genotype+condition+Genotype:condition I get the following result

[1] "Intercept"                        "Genotype_II_vs_I"          
[3] "Genotype_III_vs_I"             "condition_infected_vs_mock"      
[5] "GenotypeII.conditioninfected" "GenotypeIII.conditioninfected"  

results(dds, contrast=list( c("condition_infected_vs_mock","GenotypeII.conditioninfected")))

Does this me the result in GenotypeII after comparing with GenotypeI in infected vs mock condition I want to compare Genotype II with GenotypeI in infected vs mock condition

[Devon Ryan]

It's a bit unclear exactly what you want to compare. Is it GenotypeII vs. GenotypeI while controlling for condition? If so you don't need a contrast, it's the Genotype_II_vs_I coefficient.

[hamsasekar02]

Thank you Sir for the reply To make it more clear, I want to compare Genotype II vs Genotype I in infected vs mock condition, and also seeing the condition effect of GenotypeII with respect to Genotype I

[Devon Ryan]

I count more than one comparison in that sentence, rephrase it to include only one. You can control for various effects, but you can only extract one comparison at a time.

[hamsasekar02]

Thank you Sir, I understood that ("GenotypeII.condition infetced") will give me difference in in mock vs infected samples of GenotypeII taking care of mock vs infected levels in the reference genotype (Genotype I) . Is my understanding correct ??

[Devon Ryan]

Yes, stated differently that's the excess effect of having both GenotypeII and being infected at the same time compared to what you would expect if GenotypeII and "infected" didn't interact with each other at all.