Hello, in the example below, there are 2 conditions and 3 genotypes.

dds <- makeExampleDESeqDataSet(n=100,m=18)
dds$genotype <- factor(rep(rep(c("I","II","III"),each=3),2))
design(dds) <- ~ genotype + condition + genotype:condition
dds <- DESeq(dds)
resultsNames(dds)
# "Intercept"              "genotype_II_vs_I"       "genotype_III_vs_I"      "condition_B_vs_A"       "genotypeII.conditionB" 
# "genotypeIII.conditionB"

if I want to know if treatment B vs A difference is different in genotype III to II, will I be able to do so with the contrast function as shown below?

results(dds, contrast=list("genotypeIII.conditionB", "genotypeII.conditionB"))

It might be simpler to make II your reference genotype, then "genotypeIII.conditionB" will do what you want by itself.