Hi all,

I'm having some difficulty understanding how to interpret the results of the interaction term in a DESeq2 setup. Simply put, I have an experiment with two variables - Condition (A or B), and Treatment (Untreated or Treated). I'd like to know a few things:

1) in Condition A, what is the Treatment effect?

2) in Condition B, what is the Treatment effect?

3) what is the difference in Treatment effect between Condition A and Condition B?

For the first two, I used the
method described in the vignette, no problem.

For the 3rd question, an interaction term seems appropriate, e.g.:

Looking at the results from the interaction term:

I get something like 52 genes where the the Treatment effect is significantly different in Condition B vs Condition A. My intuition is that these 52 genes would show up in either of the first two comparisons above, since we're saying there is a significant difference in Treatment effects, doesn't that imply the effect should be significant in at least one of the two Conditions? But this isn't the case, as only 2 of the 52 genes are in either DEG list.

On the flip side, let's say ~450 genes were significant in comparison #1 and ~1000 genes in comparison #2 above. Why aren't the genes in the

I'm having some difficulty understanding how to interpret the results of the interaction term in a DESeq2 setup. Simply put, I have an experiment with two variables - Condition (A or B), and Treatment (Untreated or Treated). I'd like to know a few things:

1) in Condition A, what is the Treatment effect?

2) in Condition B, what is the Treatment effect?

3) what is the difference in Treatment effect between Condition A and Condition B?

For the first two, I used the

Code:

factor(paste0(...))

For the 3rd question, an interaction term seems appropriate, e.g.:

Code:

design = ~ Condition*Treatment

Code:

results(dds, name=c("ConditionB.TreatmentUntreated"))

On the flip side, let's say ~450 genes were significant in comparison #1 and ~1000 genes in comparison #2 above. Why aren't the genes in the

*setdiff*of these two lists, significant in the interaction term contrast? Am I thinking about this all wrong?
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