Hi, Dr Love. I am little confused about the example in ?results. The example3 in ?results is listed below

## Example 3: two conditions, three genotypes

# ~~~ Using interaction terms ~~~

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)
[1] "Intercept"              "genotype_II_vs_I"      
[3] "genotype_III_vs_I"      "condition_B_vs_A"      
[5] "genotypeII.conditionB"  "genotypeIII.conditionB"

# the condition effect for genotype I (the main effect)
results(dds, contrast=c("condition","B","A"))

# the condition effect for genotype III.
# this is the main effect *plus* the interaction term
# (the extra condition effect in genotype III compared to genotype I).
results(dds, contrast=list( c("condition_B_vs_A","genotypeIII.conditionB") ))

# the interaction term for condition effect in genotype III vs genotype I.
# this tests if the condition effect is different in III compared to I
results(dds, name="genotypeIII.conditionB")

# the interaction term for condition effect in genotype III vs genotype II.
# this tests if the condition effect is different in III compared to II
results(dds, contrast=list("genotypeIII.conditionB", "genotypeII.conditionB"))

Forgive my little konwledge about model.matrix. I haven't figured model.matrix out yet.

According to these example, I thinks the contrast=c("condition","B","A") means genotypeIB(or I say IB) - genotypeIA(or I say IA).

And the name=genotypeIII.conditionB means (IIIB - IIIA) - (IB - IA).

And according to the above explanation, the results(dds, contrast=list("genotypeIII.conditionB", "genotypeII.conditionB")) will means [(IIIB - IIIA) - (IB - IA)] - [(IIB - IIA) - (IB - IA)] = (IIIB - IIIA) - (IIB - IIA). which same as this word this tests if the condition effect is different in III compared to II

But If I apply this explanation to results(dds, contrast=list( c("condition_B_vs_A","genotypeIII.conditionB") )), this will not make sense. this will become (IB - IA) - [(IIIB - IIIA) - (IB - IA)] = 2(IB - IA) - (IIIB - IIIA).

If the descriptions of interaction terms in the manual pages or the interaction section in the vignette are not sufficient, I’d highly recommend working with a statistician to design your analysis. The specification of the design is up to the user.

You can also just provide a numeric contrast if that would be easier than calling the coefficients by name.