This is for normalizing array data for one-color agilent array using Cy3 dye using the Limma Package (http://bioinf.wehi.edu.au/limma/) copy or move all the *.txt files from Data and Scan Analyzed to raw folder modify targets.txt such that it maps each txt with sample go to scripts folder open the R script in R and run: source('normalize_summarize_Agilent_arrays_OneColor_withTargetFiles.R') Note if you edit the targets.txt file with Excel, it may screw up the return symbols and make the R script crash while reading target file. To check if excel screwed up anything. go to terminal, do: "less targets.txt" and see if you see those ^M characters appearing. Also check with "wc -l" to see the number of lines. If there is 0 lines, then Excel messed up the return symbols. To correct that: mv targets.txt targetsExcel.txt cat targetsExcel.txt | tr "\015" "\n" > targets.txt echo "" >> targets.txt wc -l targets.txt now wc -l targets should give you the correct number of lines (i.e., number samples + 1 for the header) What the script does is: it reads in target file (which map raw data to sample name) and array files to get signal matrix, then normalize across the arrays by quantile normalization. After the script there will be a tlimmaOutput folder, within it a withControl folder, within it some pdf files and some txt files. The pdf files are diagnostic plots of the log2 intensity distribution before (plotDensities_raw.pdf) and after normalization(plotDensities_after_between_norm.bgc0.pdf) The corresponding txt files (G.raw.txt and G.bgc0.norm.txt) contains the raw and normalized expression matrix respectively. And values are in log2.