I'm working on some data from scRNA-seq-based expermient in order to perform Differential Expression Analysis . I'm following the recommendations provided in DESeq2's vignette, but I still stuck with the step of setting sizeFactors from scran.
In fact, I calculated the size factors for all cells but my problem is I don't know how should I use them in the downstream steps.
Should I feed them to DESeq() or to results() , for instance, If so, how ? Because I searched in the arguments of these functions without finding any possibility to do that (to my limited knowledge of course).
Please give me some insights.
Thanks in advance !