Combining mRNA and total RNA studies
I am trying to combine two different studies with the fastq files processed using the same pipeline. Is there any measure to take heed of apart from normalization and batch correction? I am currently using TPM normalization and batch correction using CombatSeq.
Apart from this, is only batch correction required before DESeq2 in case I want to combine the two studies or is using batch variable in the design is enough?
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