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

Normalizing separately is likely to lock in a bias that would be removed if you normalize together. So, I would be more inclined to believe the (fewer) differentially expressed genes that you find when normalizing together. On 7/25/2012 6:07 AM, Cytochalasin wrote: > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor