Abstract The increasing use of high-throughput gene expression quantification technologies over the last two decades and the fact that most of the published studies are stored in public databases has triggered an explosion of studies available through public repositories. All this information offers an invaluable resource for reuse to generate new knowledge and scientific findings. In this context, great interest has been focused on meta-analysis methods to integrate and jointly analyze different gene expression datasets. In this work, we describe the main steps in the gene expression meta-analysis, from data preparation to the state-of-the art statistical methods. We also analyze the main types of applications and problems that can be approached in gene expression meta-analysis studies and provide a comparative overview of the available software and bioinformatics tools. Moreover, a practical guide for choosing the most appropriate method in each case is also provided.