Differential Gene Expression Analysis Across Cell Types Split Into Individual Datasets - Accounting for Technical Variations
I would like to run a joint differential gene expression (DEG) analysis to compare different cell types across multiple datasets. Each dataset represents one cell type that was isolated experimentally. I combined the different datasets and ran DEG analysis between them. My worry is that this doesn't account for batch effects/technical variations between datasets. I also understood that I cannot use integration methods since there is no overlapping population between datasets (i.e. each dataset = different cell type). Any way I can still account for technical variations?
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