Hi Balazs, To which MAS5 do you refer? The implementation in Affy's software, or the mas5() function in the affy package? If mas5(), then the scale value is set at 500, so there shouldn't be a difference between any chip type. See ?affy.scalevalue.exprSet. Best, Jim Dr Balazs Gyorffy wrote: > Hi! > > MAS5 normalizes to different averages when using HGU133A (to 800) and HGU133Aplus2 (to 1500) chips. Can I set the target average during normalization? > > Thanks > Balazs > > > > [[alternative HTML version deleted]] > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826