I have been analysing RNA-seq data using DESEQ2, but keep being asked the same question. Can you / why haven't you incorporated the spike-ins for normalisation.
From my perspective, this isn't necessary due to the tests DESEQ2 runs, which consider composition bias/sequencing depth, which spike-in normalisation doesn't. Is this right? If not, does anyone know a way spike-ins can be incorporated into DESEQ2 analysis?
For context, I have been using the DESeqDataSetFromHTSeqCount function as I have read count files produced from my alignment script.
Thanks in advance, C