Hi Group, I have the MAS 5 normalised intensity values as an expression set which I got from the series matrix file deposited in the geo with 3 control and 3 treated(HG_133A). Now I need to write the code for setting the trimmed mean target intensity of each array to 100.I would also like to know what is the meaning of "The trimmed mean target intensity of each array was arbitrarily set to 100." Session info R version 2.12.0 (2010-10-15) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 code: >source("http://bioconductor.org/biocLite.R") >biocLite() >library(affy) >exprs <- as.matrix(read.table("GSEXXXX_series_matrix.txt",header = TRUE,sep = "\t", row.names = 1, as.is = TRUE)). Waiting for your response, Thanks, Viritha [[alternative HTML version deleted]]