I've fit a stratified Cox proportional hazards model to some survival data, where I've stratified by a potential confounder which is the batch the data comes from (there are three batches).
Now, I'd like to externally validate this model on a new set of data, that also come from the three batches (independent samples though). Should I be using the strata information in this prediction? My thoughts are to exclude the strata, as I want to remove this confounding factor and not artificially inflate my predictive value (C-index etc).
Is this correct?
Edit for clarification:
Say I'm developing a diagnostic test for some disease, using a stratified Cox model to account for a confounder (a batch effect like which hospital the data was collected at). Now, if I go to apply this test in the real world, a new individual won't have the batch effect associated with my study, so there's no point in assigning them to some pre-defined stratum.