Zebrafish spotted-microarray for genome-wide expression profiling experiments: data acquisition and analysis.

In expression microarray experiments, post-hybridization procedures involving data acquisition and analysis are mainly computational and hence are described as "dry-lab procedures." The aim of these procedures is to acquire the fluorescent signals representing the relative abundance of tens of thousands of RNA species in samples with biological interest, and transform them into meaningful data with biological significance. These procedures begin with image and data acquisition followed by data normalization and processing, and thereafter primary and secondary data analyses. Although the actual data analysis is carried out after the wet-lab procedures, the strategy for data analysis should be planned prior to wet lab procedures when designing the experiment, to ensure effective downstream data handling and interpretation. Principal steps and advisory notes for acquiring, processing, and analyzing data that are commonly associated with various zebrafish expression profiling experiments are described in this chapter.