There are several packages and tools for this purpuse
AMDA is freely available as an R package for the automated microarray data analysis, available under the GPL license. The package as well as an example analysis report can be downloaded in the...
You can try this tutorial from university of chicago http://cri.uchicago.edu/wp-content/uploads/2012/05/Analysis-of-Microrrays-with-R-and-Bioconductor.pdf