Material for exam: lecture slides + the following material ----------------------------------------------------------- Biology: Draghici Ch 1 Microarray technology: Draghici Ch 2, 3 Preprocessing: Draghici Ch 3, 4, 8, 12 + (Wu et al. JASA, 2004, 99,468:909-917, http://www.genomine.org/publications.html) (GCRMA) Basic hypothesis testing: Draghici Ch 4,5,6,7,9,13 + (Storey, 2002, JRSSB, 64:479-498) (q-values) + (Efron and Tibshirani, 2007, Annals of statistics, http://www-stat.stanford.edu/~tibs/ ) Visualization: Draghici Ch 10 + Gentleman at al., Bioinformatics and Computational Biology Solutions Using R and Bioconductor: Ch 3 Clustering: Draghici Ch 11 + Madeira and Oliveira, TCBB, 1,1,2004 + Manly: Randomization, Bootstrap and Monte Carlo Methods in Biology, pp. 1-9 (randomization), 41-51 (bootstrap) Classification: Theodoridis and Koutroumbas, Pattern Recognition: Ch 1,2,3.1,3.2,3.6,4.17-4.19,5.1-5.7 + Diaz-Uriarte et al. Bioinformatics 2006 + Guyon et al. JMLR, 2003 (further reading) + S. Haykin: Neural Networks:pp. 217-218 (cross-validation). Mass spectrometry and systems biology: Katajamaa and Oresic, 2005, BMC Bioinformatics + Listgarten and Emili, 2005, Molecular & Cellular Proteomics. ------------------------------------------------------------------- The exam: 5 questions, max 30 points, 0-2 points from exercise work, over ~15 points: pass, The material additional to Dragichi is available from room (B336), grey chest of drawers in the left corner, yellow folder in the second top-most drawer. NOTE! There is a lot of material: You do not need to know details by heart. Instead, focus on the basic ideas: what are the key ideas in this method, why this method is good, what differentiates it from the others, what are the weaknesses.