Microarrays allow the analysis of many different genes at once. While this is an impressive feat when it works, it often does not. It's very easy to design a bad microarray experiment or just to get bad results. A large part of microarray analysis therefore involves quality; how good is the microarray, how good is the result1.
The main part of this practical, then, is involved with analysing and discussing the quality of the microarray chips; a lot of what you will do does not actually relate to the biological questions that we are trying to answer, rather just to making sure that the microarray chips were not damaged, that the experiment is a good one.
1. The supervisor of my first project told me at one point, "Never under-estimate the ability to mess up" (the original phrase was a bit stronger than this...). It's worth a point worth remembering with microarray analysis more than most.