Although ultrahigh-throughput RNA-Sequencing has become the dominant technology for genome-wide transcriptional profiling, the vast majority of RNA-Seq studies typically profile only tens of samples, and most analytical pipelines are optimized for these smaller studies. However, projects are generating ever-larger data sets comprising RNA-Seq data from hundreds or thousands of samples, often collected at multiple centers and from diverse tissues. These complex data sets present significant analytical challenges due to batch and tissue effects, but provide the opportunity to revisit the assumptions and methods that we use to preprocess, normalize, and filter RNA-Seq data - critical first steps for any subsequent analysis. We find analysis of large RNA-Seq data sets requires both careful quality control and that one account for sparsity due to the heterogeneity intrinsic in multi-group studies. An R package instantiating our method for large-scale RNA-Seq normalization and preprocessing, YARN, is available at bioconductor.org/packages/yarn.