Auto-Alignment Issues

Cause

Resolution

BeadChips not properly seated in iScan Reader tray.

Eject the tray and remove the BeadChips. Make sure the back of the BeadChips are free of coating. If necessary, clean the backside of the BeadChips. Reload the BeadChips, making sure that they are secure and flat in the carrier. Reload the carrier in the iScan Reader tray. Make sure that the carrier is flat and aligned. Make sure that the notches on the tray match the beads on the adapter plate and the front presses against the front alignment features.

Carrier tray not properly seated in iScan Reader tray.

Eject the tray. Remove the carrier from the tray. Replace the carrier in the iScan Reader tray and ensure proper seating.

Sections are broken or dirty.

Eject the BeadChips and visually inspect sections. Make sure that no sections are broken or dirty. Follow lab protocols for cleaning sections, and report broken sections to the responsible scientist. Try scanning the BeadChip again.

Lasers are no longer be within factory specifications.

Contact Illumina Technical Support to recalibrate the iScan Reader and rebalance lasers.

Optical-mechanical failure.

Call Illumina Technical Support to investigate this issue further.

Cannot find fiducials.

Clean fiducials with an ethanol wipe and rescan. Sometimes the protective coating on the BeadChips inhibits the lasers from finding fiducials.

Camera times out.

Perform a power cycle.

System enters an infinite autotilt loop.

Perform a power cycle.

Instrument cannot focus.

Inability to focus can result from using a different adapter tray. Replace original adapter tray.

Cause

Resolution

Problems during BeadChip preparation can result in some sections appearing too dim to perform registration and bead intensity extraction.

Contact the responsible scientist to discuss the history of the assay preparation for the BeadChips and the expectation of the scientist. Evaluate the image output of nearby images using images stored in the workspace for this BeadChip. If the issue is not resolved, contact Illumina Technical Support.

BeadChips have been exposed to adverse environmental conditions.

Evaluate the effect of the environment on signal quality pertaining to the BeadChip sections.

Sections are broken or dirty.

Eject the BeadChips and inspect sections to make sure that none are broken or dirty. Follow lab protocols for cleaning sections, and report broken sections to the responsible scientist. Try scanning the BeadChip again.

Low intensity or poor-performing samples.

Review scan metrics to uncover potential issues.

Stripe turns red instead of green.

One of the four swaths within the stripe is not imaged correctly. Check to make sure that the swath is in focused and the BeadChip is properly aligned.

Cause

Resolution

BeadChips do not lie flat within the carrier.

Remove the BeadChip carrier from the iScan Reader tray and reseat the BeadChips. Make sure that they lie flat within the slots on the carrier. For more information, refer to Load BeadChips.

The SDF file chosen does not match the BeadChip type.

Make sure that the SDF file selected matches the BeadChip type. If it does not, then rescan the BeadChip using the correct SDF file.

Camera has timed out.

Power-cycle the PC and scanner.