I have (matched) case-control data. The data is collected in batches in such a way that the batch determines some quality of the data (there is a 'batch' effect).
Also, the cases and controls were not randomly distributed among these batches. So batch 1 contains only cases, batch 2 contains only controls, batch 3 is mostly cases (a couple controls) and batch 4 is mostly controls (a couple cases).
I'm trying to do logistic regression to determine if some covariates are associated with disease. I need to control for the batch effect. Will the fact that the cases/controls are not randomly distributed among the batches have a negative impact on my model if I include the batch as a covariate?
From my reading it appears that can be somewhat of a common problem called Quasi or Complete separation.