Hi Peder, I am trying to use your script for doing two channel miRNA exiqon data and i am ending up with following error. Cy3.norm <- apply(cy3.channel,2,function(v){tapply(v,names(v),function(x){median(x ,na.rm=TRUE)})}) Error in tapply(v, names(v), function(x) { : arguments must have same length any help is appreciated Thanks Ashwin [[alternative HTML version deleted]]