Combinations of factors not observed, non-full rank design matrix. How to explain to investigator?

So I am helping someone with a differential expression analysis, there are only 10 samples, two variables with two levels each. Let's say Sex (M/F) and Age (Old/Young). They originally wanted to model: ~ sex + age + sex*age

However Sex = F & Age = Young does not exist in

the data (no sample with that combination observed), so model matrix is not full rank and DESEQ model can't be specified.

I warned them of this and their solution was to concat the Sex and Age variables to a new var (let's just say V3) and run the model with only ~


I know this technically works... (as in the design matrix is full rank), but I also know it isn't a great idea, basically bc we are extrapolating and are now unable to make any claims about M vs For Old vs. Young.

Any tips on how to explain this to the investigators?
  • Savionf Savionf

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