Generated Files
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After images are scanned, they are registered and intensities are extracted for every bead type.
The following sections describe the files that are generated. Information about scan or registration failures is also provided.
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.
Images
Each image file (*.jpeg
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.
