Dear all, please would you confirm the following :
shall we have as input in DEseq2 all the RNA-seq data that was generated in 4 different conditions (let's say):
<> C1 <> C2 <> C3 <> C4
when the baseMean X is computed, is it supposed to be the same, regardless of the contrasts that we make ?
shall we extract the contrast C1 vs C2 : the reported baseMean is supposed the same X as above ?
we extract the contrast C3 vs C4 : then the reported baseMean is still X, correct ?
thanks a lot !