Agilent-gpr-scripts is a project mainly written in R, it's free.
agilent-gpr-scripts raw (put your gpr files and gal file) normalized (created)
goto agilent-gpr-scripts open R, source("normalizeAgilentGPRFormattedArrayData.R")
processing background correct "none" within array "loess" across array "quantile"
creates: log2 expression value
geneName Rvalues... (log2) Gvalues... (log2)