How the iScan determines beadchip type and which scan settings file to apply

For every beadchip, the DMAP folder contains an .sdf file, which describes the physical dimensions of the beadchip in order to set the scanner to scan the beadchip properly. At the end of the .sdf file, a line assigns the assay type. Following is a screenshot of the end of an .sdf file for a GSA24v3.0 beadchip:

Note: although the Global Screening Array is an HTS beadchip, LCG and HTS beadchips are processed in very similar ways, with the major difference being the number of samples per chip (LCG have 8 or fewer samples per chip, HTS have 24 samples), hence both are classified by the iScan as LCG assay type beadchips, as they require the same scan parameters.

The choice of which scan settings file to apply for a given assay type is made in the iScan software through the Assay Mapping Tab in the options menu. In the scanner software, select the chevron to access the main menu, then select Tools > Options...

Next, select the Assay Mapping tab.

The Assay Mapping tab contains two columns, the "Assay Name" and "Scan Settings" columns. The "Assay Name" column lists the Assay types available for scanning on the iScan, and the "Scan Settings" lists the scan settings file that is currently assigned to the given assay types.

Note: upon selecting the individual Scan Settings assignments in the table, the entries are selectable through a drop-down menu, accessed by the carat on the right side of the entry. While it is possible to assign any existing scan settings file to any given Assay Name, Illumina strongly recommends against changing the settings, as any changes may result in suboptimal scanning results.

Reference:

iScan System Product Documentation