I have 2 batches, batch 1 having 4 samples (normal tissue) and batch 2 having 8 samples (normal tissue). These 2 batches are different in library size preparation (one is unstranded and other is reverse stranded) rna-seq datasets downloaded from GEO. I have a third dataset from TCGA (cancer tissue). And I wish to perform DESEq2 analysis. How do I combine them true DGEs? Should I use Combat-seq within DESeq2, if yes then what will be the code?
I have 2 batches, batch 1 having 4 samples (normal tissue) and batch 2 having 8 samples (normal tissue). These 2 batches are different in library size preparation (one is unstranded and other is reverse stranded) rna-seq datasets downloaded from GEO. I have a third dataset from TCGA (cancer tissue). And I wish to perform DESEq2 analysis. How do I combine them true DGEs? Should I use Combat-seq within DESeq2, if yes then what will be the code?