running combat-seq with DESeq2

[Mercilena]

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?

[rohanr3ji]

Batch correcting is preferred when merging batches with samples of the condition you would like to study (In your case the condition of study is Normal and Cancer). Since there are no cancer tissues in the batches 1 and 2, the batch correction will not be effective. It will remove the biological difference you would want to study between the normal and cancer tissue.