Best Preprocessing Approach for Tissue Microarray Data: Separate or Post-Merger Normalization?

Question

[rk.khayami94]

I have multiple microarray datasets from various tissues, all generated using the same platform, and I'm aiming to create a model that classifies each tissue based on the methylation of probes.

Should I first normalize each dataset separately and then merge them, followed by removing the batch effect? Or would it be more effective to merge the datasets first and then perform the normalization process?