I have patient data (microarray data > 100 samples, very noisy) - and as always there are many factors (disease/control, infection, age, sex, treatment, cohort, pmi, batch/scandate).
So my question is basically a generell question concerning combat. I am interested in two biological variables - disease/control and infection. Should/can I correct for the others by running combat sequentially? If yes, what about the order? This does influence the outcome.
Or is multiple batch correction basically overfitting the data?
Thank you very much!