This practical is based around the analysis of differential gene expression in two different strains of Soybean. This should give you practical experience of analysing real microarray data.
The practical is based around a recent paper from Briefings in Bioinformatics. You can read the full paper here. We have made a few minor modifications to the code (i.e. fixing the broken bits)
Brief Bioinform. 2007 Nov;8(6):415-31. Epub 2007 Sep 29
A microarray analysis for differential gene expression in the soybean genome
using Bioconductor and R.
Gregory Alvord W, Roayaei JA, Quiñones OA, Schneider KT.
doi:10.1093/bib/bbm043