Hi there,

this has been asked a couple of times, but I'm having issues troubleshooting this.

I have following metadata:

When I then run the deisng formula design = ~ condition + timepoint + condition:timepoint I get following error:

the model matrix is not full rank, so the model cannot be fit as specified. Levels or combinations of levels without any samples have resulted in column(s) of zeros in the model matrix.

I suppose the reason I get the error is because in the experimental desing only one timepoint was included for the mock condition?! Basically what I want to compare are the timepoints of the infected conditions contrasted to the single mock condition.

Thanks!

Just combine the two variables into one and make pairwise comparisons, see the first paragraph of the interaction section of the vignette.