Generated Files

Registration

Registration identifies beads by correlating their locations on the scanned image with information in the bead map (*.dmap) file.

Intensity Data

The intensity extraction process determines the intensity values for every bead on the image. Statistics are generated for every bead type based on the intensities of the replicate beads for that type. Extracted information is saved in intensity data (*.idat) files.

IDAT files are only created for samples that have all their stripes scanned. These files are not created when scanning individual stripes within a sample section on a BeadChip.

An IDAT file is generated when the registration data for all stripes is present for a given sample. If all stripes are scanned, regardless of their results for registration or other metrics, an IDAT file is always generated. If a hardware error occurs whereby at least one stripe in the sample is not scanned, then no IDAT file is generated for the sample.

Normalized Data

If the AutoConvert feature was enabled for the scan, iCS normalizes the data in the IDAT files and generates genotype calls from the normalized data. The normalized data and genotype calls are saved in genotype call (*.gtc) files. For more information, refer to Generate Normalized Data and Genotype Calls

The IDAT and (if applicable) GTC files are saved on the instrument control computer or network under the BeadChip ID (barcode identifier) subfolder, in the output path folder.

Scanner Configuration Information

The Effective.cfg file is created at the start of a scan. The file contains all the scanner configuration information for the current scan. It is saved in the BeadChip ID folder in the output path.

Images

Each image file (*.jpeg or *tiff) is saved on the instrument control computer or network. The image files are saved under the BeadChip ID (barcode identifier) folder in the output path folder. File names for each individual node are generated based on the position of the section in the BeadChip.

The files are named according to the following nomenclature: ID_LABEL_STRIPE_SWATH_CHANNEL.EXTENSION

File Name Component	Description
ID	The serial number (or barcode) of the BeadChip.
Label	Refers to the location of the sample on the BeadChip.
Stripe	Numbered section starting from the top left of a sample on a BeadChip.
Swath	Some BeadChip stripes are imaged using two or three smaller stripes, known as swaths. The name of the swath refers to the location of the image in each stripe. In a 2-swath stripe, for example, Swath 1 is the image of the upper half of the stripe and Swath 2 is the image of the lower half of the stripe.
Channel	RED or GRN for red or green channels respectively.
Extension	Uncompressed images—.tiff Compressed images—.jpeg

Scan or Registration Failure

Registration and extraction are critical to obtaining results from experiments.

If one or more stripes fail scanning or registration in a sample section, you can rescan the stripes by selecting Rescan on the iCS Review screen. Upon rescan, new intensity data files are generated.

When failed sections on a BeadChip are immediately rescanned within the current scan session, new image files are created only for the sections that are scanned. When an entire BeadChip is rescanned, all image files are recreated.

If you select Done on the Review screen without rescanning the failed sections, the IDAT files are created without data from the failed section, which could reduce assay performance or results. Rescan the entire sample section during a future session to generate complete IDAT files.

When an entire BeadChip or sections of a BeadChip are rescanned during another session, new metrics and IDAT/GTC and QC files are created with each rescan. These new files overwrite existing files. To prevent files from being overwritten, save the rescan data in another output data folder.