Raw and processed data files
ArrayExpress stores raw data files, and processed data files or matrices (usually in the form of tab-delimited text files) for microarray experiments (Figure 6).
For NGS experiments, all processed sequence files (e.g. BAM alignment files) and derived data (e.g. normalised read count matrices) are stored directly in the ArrayExpress database. The raw sequence files are deposited in the European Nucleotide Archive (ENA) (7) and appear as direct links in ArrayExpress. The format of raw data files varies depending on the platform used (array manufacturer, sequencer machine, etc.).
Figure 6 Types of experimental data that are stored in ArrayExpress.