talking about the standard normalization methods of RNA-seq data as implemented in limma, edgeR or DeSeq2 :
is there any modification we shall do in the normalization method when analyzing the RNA-seq data of these 3 sets of samples :
a) control b) over-expressing X protein (Wild Type) WT b) over-expressing X protein (Mutant) MUT
taking into consideration the fact that XproteinWT may have very different levels of expression that XproteinMUTANT
(i.e. 1.5-2x fold difference) ?
thanks a lot,