I think this microarray pipeline tutorial will be much useful for you .. http://www.bioinfo.no/training/introduction-to-microarray-technology-9.-10.-may-2011/Microarray%20pipeline_2011.pdf
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...