Metadata for microarray experiments
There is a third type of MAGE-TAB file, which is relevant for microarray experiments. All microarray experiments are additionally associated with an Array Design Format (ADF) file (Figure 5).
Figure 5 The Array Design Format describes the layout of the array used for microarray experiments in ArrayExpress.
The ADF describes how a microarray was manufactured and what was printed or synthesised on the array. Each position of the array or "probe" is annotated with information like the gene ID or the genomic position for which the probe is specific. This information is crucial for analysis of microarray raw data.
For commercially available microarrays, this file is provided by the array manufacturer and is often already archived in ArrayExpress.
Custom array designs need to be submitted to ArrayExpress before they can be associated with an experiment.