Dear all,

I am trying do performed some analysis with DESeq2, using a model with 
interaction therms, but I have a hard time understanding what DESeq2 is 
doing exactly (I am also not very familiar with R notation and have a 
hard time understanding it too, sorry).

What I want to do correspond to the what is described in section "3.3 
Interactions" of the vignette " Differential analysis of count data - 
the DESeq2 package", i.e. one model with 3groups-2treatments, and one 
with 2groups-2treatments (2 different analysis).

- in the first example (p21, comparing "patient4.treatmentOHT" to 
"patient4.treatmentControl"), what will be exactly the numerator and 
denominators? How is the log2FoldChange calculated in this case? (I have 
read section 4.2 and the pre-submission on bioArxiv, but I am still not 
sure of what is calculated in this case ; I also do nto really 
understand the sentence " Note that the log2 fold change for treatment 
of OHT over control for patient 4 is the interaction effect above in 
addition to the main effect of treatment OHT over control", p21).

- in the second example p22, with only 2groups and 2 treatment, to what 
contrast does "patient2.treatmentOHT" correspond to? The specific effect 
of treatment OHT on patient 2, taking into account the general effect of 
OHT?

Many thanks in advance!
Samuel


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