I would like to clarify some concepts about DESeq normalization:
1)How does DESeq account for RNA compostion in the "median of ratios" method (if so, in which step of the code/formula)?
2)Kind of stats question, why is the geometric mean more appropiate than arithmetic mean for the
pseudo-sample created to obtain the size factors?
3)How reliable is DESeq on ~10 samples per condition with no biological nor technical
replicates. I've read in a previous post there is no support for this scenario. Sequencing is
expensive, does it means that it doesn't make sense to use DESeq2 for DEG in this case,
what would you recommend?
Thank you so much in advance,