Hi,

probably a silly question but is there a difference between these two models in DESeq2:

counts ~ Condition : Generation

counts ~ Condition * Generation

They both model the interaction between condition and generation, am I correct?

However, when I try to run the upper model, I get an error message:

Error in checkFullRank(modelMatrix) :
  the model matrix is not full rank, so the model cannot be fit as specified.
  One or more variables or interaction terms in the design formula are linear
  combinations of the others and must be removed.

The model with the asterisk works just fine.

Thanks!

From ?formula:

"In addition to + and :, a number of other operators are useful in model formulae. The * operator denotes factor crossing: a*b interpreted as a+b+a:b."

So it doesn't really make sense to have only an interaction term (~ a:b). Interaction terms are usually meaningful in designs with main effect terms.