An increasing amount of microarray gene expression data sets is available through public repositories. Their huge potential in making new findings is yet to be unlocked by making them available for large-scale analysis. In order to do so it is essential that independent studies designed for similar biological problems can be integrated, so that new insights can be obtained. These insights would remain undiscovered when analyzing the individual data sets because it is well known that the small number of biological samples used per experiment is a bottleneck in genomic analysis. By increasing the number of samples the statistical power is increased and more general and reliable conclusions can be drawn. In this work, two different approaches for conducting large-scale analysis of microarray gene expression data—meta-analysis and data merging—are compared in the context of the identification of cancer-related biomarkers, by analyzing six independent lung cancer studies. Within this study, we investigate the hypothesis that analyzing large cohorts of samples resulting in merging independent data sets designed to study the same biological problem results in lower false discovery rates than analyzing the same data sets within a more conservative meta-analysis approach.