[BioC] Normalization of array leads to decrease in number of differentially expressed genes

[Cytochalasin]

Hi all,

I performed normalization on my array data (I use qPCR array of 384
wells), and if I normalize within replicates of all conditions(each
condition normalized separately) , I get more differentially expressed
genes that if I normalize all data together., How may I found that
which result is more accurate?

Thank you in advance