Abstract | Installation instructions | Data retrieval | Searching for ontology terms | Identifying datasets associated with specific ontology terms | Obtaining dataset-level metadata | Obtaining gene-expression data (as SummarizedExperiment objects) | Example 1: Plotting gene-expression values | Example 2: Using metadata to create a heatmap | Example 3: Using Feature Data | Session Info

Background | How to produce SCAN estimates for Affymetrix microarrays | How to produce SCAN estimates for Agilent two-color microarrays | How to produce UPC estimates for microarrays or RNA-Seq | Reducing processing time for Affymetrix microarray normalization | Conclusion