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 Services/Bioinformatics section of the Genopolis http://www.genopolis.it/
Genopolis supports two oligonucleotide microarray whole-genome gene-expression platforms—Affymetrix® and Illumina®—to offer a range of cost and performance options suitable for a variety of experimental questions.Paper http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1534071/
GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data http://www.gepas.org/
Paper http://nar.oxfordjournals.org/content/33/suppl_2/W616.abstract
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
Hi Govardhan,
The bioconductor search for microarray returned 3448 results at http://www.bioconductor.org/help/search/index.html?q=microarray
Many of them will fix for you research requirement.
Thanks
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