Analysis of DNA microarray data. Part II: Quantification and analysis of gene expression. The first step in a DNA microarray experiment is to define the biological question to be addressed and the selection of an appropriate experimental design. The experiment, however, does not end after the samples are processed and hybridized to the chips, since the fluorescent images that are its primary result have to undergo a data analysis process to assign expression values, using the mathematical-statistical methods suited to the goals of the study. Here a particular emphasis is made on the methodology used to quantify and analyze gene expression data. The most frequently used programs are briefly described and working plans are proposed for some of the most common experimental objectives. Additionally, we discuss and comment the applications of this technology in the field of Oncology, where it has enabled the discovery and classification of new cancer subtypes, and has helped to identify new therapeutic targets, as well as improving the prediction of disease stages.