Dear all,

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 !

You can conveniently convert your SingleCellExperiment to a DESeqDataSet, see https://bioconductor.org/packages/devel/bioc/vignettes/scran/inst/doc/scran.html#8_Converting_to_other_formats, which makes sure your size factors end up in the right slot of the new object. I think you only have to set a design then using design(dds) <- ~whatever+you:want.