I am using both edgeR and DESeq2 to normalize raw counts (it's not RNA-seq data or 16S amplicon seq data...but it is amplicon seq data). I just need to normalize them before creating a visualization. It's preliminary work; so the parts of these packages that calculate differential expression are not useful to me.
I have two sets of scaling factors (from edgeR using the TMM and RLE methods). My question is what is the correct approach for applying these scaling factors to my raw counts. Is it:
raw count / scaling factor
raw count / (library size * scaling factor)
I've been researching these methods and so far I have seen it both ways. I'm still not sure how to just get normalization factors from DESeq2, as I just got that package installed yesterday evening. But I've kept the DESeq2 tag because the question applies to both and if anyone has advice regarding DESeq2 that could be helpful to me and others.
Rookie question: the dispersion calculation would make sense for evaluating DE, not as part of the normalization, right?
Thanks for the help.