NewAgilentOneColorTemplates is a project mainly written in R, it's free.
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 "