Hello, I am doing a RNA-Seq DE analysis with DESeq2 and I was told to not consider the gene basal expression level as 0, so, how would I do that step? Are they referring to the relevel function in DESeq2? or setting the control samples as the targets of the comparison? Or is there more to it that i am not aware of?
Also, would results differ a lot if I do the analysis as indicated in the DESeq2 tutorial and not do the "not considering basal expression level as 0" step ?