I am planning to preprocess 40 microarray series comprising of 1200 samples. For all these series, mRNAs were quantified using same platform "GPL570". I thought of using ComBat for batch effect correction prior to differential analysis. But, I dont know at which step that I need to use comBat.
Which is the correct procedure?
Background correction, Normalization , filtering the probes based on present and absent calls (panp package in R) and combat
Backgroung correction, Normalization, batch effect removal using combat and filtering the probes based on present and absent calls (panp package in R).
There is no defined method and Each paper follows different methodology. Please let me know.
Thanking you for your time.