The central dogma of molecular biology -- What are microarrays and how do they work? -- Gene function and drug discovery -- Data generation, processing and analysis: an overview -- Data management -- Experimental design -- Experimental objectives and features of microarray data -- General principles of experimental design -- Reducing the number of variables -- Time courses vs. independent data points -- Replicates and repeated measurements -- Reference samples -- Exogenous ('spiked-in') controls -- Dual labelling/dye swapping -- Validation of results -- Choice and preparation of samples -- Obtaining the appropriate sample -- Strain background -- Mutants -- Reagents -- Sample and sample composition -- Small amounts of sample: RNA amplification and pooling -- Preparation of the labelled extract -- Assessing the quality of the labelled extract -- Choice and design of arrays -- Choice of array platform -- Oligonucleotides vs. PCR products -- Replicate, guide and control features -- Cross-hybridisation -- Hybridisation, scanning and quality control -- Long-term considerations -- Record keeping -- Standardisation -- Image processing, normalisation and data transformation -- Preliminary processing of the data -- Image analysis -- Measuring and reporting expression -- Saturated pixels -- The appropriate number of pixels -- Estimating background -- Reporting expression with Affymetrix GeneChips -- Expression ratios: the starting point for sample comparison -- Transformations of the expression ratio.