immunedeconv for RNAseq data
Hi, I am performing RNAseq meta analysis and I would like to do immunedeconv methods (MCPcounter, xCell, Cibersort, ESTIMATE), but I don't know which data to import. With meta analysis I started with raw counts. My consideration is if I should to immunedeconv before batch effect correction for each dataset(if yes should I use raw counts or vst/log2 transformed counts)t, or after correction on metacohort (if yes, should I use DESeq2 norm data or raw counts or vst/log2 transformed data). Thank you in advance for your response and help!
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