Abstract | Introduction | Gene expression profiling of the mouse mammary gland | Analysis of RNA-seq data with EGSEA | Reading, preprocessing and normalisation of RNA-seq data | Gene set testing | 1. Exploring, selecting and indexing gene set collections | 2. Configuring EGSEA | 3. Ensemble testing with EGSEA | Classes used to manage the results | 4. Reporting EGSEA results | Getting top ranked gene sets | Visualizing results at the gene set level | Visualizing results at the experiment level | Creating an HTML report of the results | Analysis of microarray data with EGSEA | Reading, preprocessing and normalisation of microarray data | Setting up the linear model for EGSEA testing | 1. Creating gene set collection indexes | 2. Configuring and 3. Testing with EGSEA | Discussion | Software and code used | Competing interests | Grant information | Acknowledgements | References