[BioC] DESeq normalisation strategy

[Davide Cittaro]

Dear list, 
I've been reading about DESeq normalization strategy and, as far as I understand, it works on a sample basis: counts for each samples are normalized according to a factor calculated using the geometric mean of the counts.
Three questions:
- is this strategy robust when comparing samples with extremely different library sizes?
- If I wanted to calculate cpm on normalized counts, should I rescale the library size according to the sizeFactor?
- counts are calculated on genomic intervals, would the same approach make sense if I use counts on single nucleotides?
Thanks

d