First of all you need to get familiar with R environment. There are many tutorials out there.

Bioconductor packages you use for analysis depends on the platform used for the data generation for the best results and sometimes integration of different packages into pipeline is needed. In a simple way, you may need to do Data preprocessing (includes filtering low quality probes), normalization, performing statistical tests to find Differentially expressed genes. You can do other things once you get the gene list within a statistical significance cut-off.

For example read this user guide of limma, a bioconductor package for microarray data analysis, followed by this, how the gene set in your hand is useful further.