Hello Dr. Peder Wong, I am trying to follow the steps you mentioned for exiqon data analysis and would like to know that is the object *Logratio *is considered to be normalized data that can be used for further analysis work?? rownames(RG) <- RG$genes[,6] #I use that to sum over spot replicates RGb = backgroundCorrect(RG, method="normexp", offset=50) cy3.channel = RGb$R cy3.channel.norm =normalizeBetweenArrays(log2(cy3.channel), method="quantile") #this is the Logscaled Cy3 data with four spots per probe cy5.channel = RGb$G cy5.channel.norm =normalizeBetweenArrays(log2(cy5.channel), method="quantile") #this is the Logscaled Cy5 data with four spots per probe MA = normalizeWithinArrays(RGb, method="loess", weights=RGb$weights) log.ratio <- MA$M # this is the Ratio data with four spots per probe #The median of the replicate probes: Cy3.norm <- apply(cy3.channel,2,function(v){tapply(v,names(v),function(x){median(x ,n a.rm=TRUE)})}) Cy5.norm <- apply(cy5.channel,2,function(v){tapply(v,names(v),function(x){median(x ,n a.rm=TRUE)})}) *LogRatio <- apply(logratio,2,function(v){tapply(v,names(v),function(x){median(x,na .r m=TRUE)})})* ** *Thanks* *Ashwin * [[alternative HTML version deleted]]