1. Final Project Everybody still registered for the grade who did not have their own project will receive an email with file names to be used for their project This will consist of the list of files with microarray data which will be located at http://eh3.uc.edu/FinalProject2006/ and will look something like: Example Treatment combinations: Nic-WT72hr_2... Nickel treated; Wild Type; After 72 hours; Replicate 2 Nic-Mt1Mt2(-/-)03hr_1... Nickel treated; Knockout; After 3 hours; Replicate 1 Also spot type descriptions will be given in http://eh3.uc.edu/FinalProject2006/SpotTypes.txt You will need to construct your own "targets" file (hint: copy and paste from the email)

2. Final Project Project consists of the in-depth analysis of the experiment that includes at minimum: Data import, processing and normalization Statistical analysis to identify differentially expressed genes. Statistical analysis should include simple paired t- test analysis (using limma or not), three-way Anova analysis that factors out the dye effect, corresponding empirical Bayes analyses and the comparison of results. Identifying "Functional clusters" defined by GO that correlate with the upregulated and downregulated groups of genes using either R or Ease You need to use the functional clustering to choose between models with and without factoring out the gene- specific dye effects

3. Final Project Project reports will be graded based on completeness of the analysis, correctness of analysis and conclusions and the overall quality of the report itself. I will post a typical complete project from last year on Blackboard by the end of this week. Report should include CLEAN R-code that does the work and the corresponding outputs, plots, etc. This can be given separately or embedded within the project itself. Reports should be submitted BY EMAIL, by March Midnight on March 17. If you have a good reason why you would not be able to submit the project by that time, you need to tell me that at least TWO DAYS before the deadline.

4. Reminder of the course Cluster analysis Classification Statistical model for regulatory motifs