Troubleshooting the GenomeStudio Error “Index Was Outside the Bounds of the Array”

The GenomeStudio error “Index was outside the bounds of the array” is most commonly encountered during project creation, when GenomeStudio attempts to read and organize input data files. This error typically indicates that the software is trying to access data elements that are missing, mismatched, or improperly formatted within the project inputs. It is typically triggered when GenomeStudio is unable to locate or correctly interpret required data elements during project creation.

Figure 1. GenomeStudio error "Index was outside the bounds of the array"

Common causes include:

• Missing or corrupted IDAT files, preventing GenomeStudio from accessing expected data points.

• Incorrect manifest file selection, where the selected file does not correspond to the Infinium BeadChip type and/or version used.

• Incorrect cluster file selection, where the cluster file does not match the BeadChip type and/or version, leading to inconsistencies during data processing.

To resolve the “Index was outside the bounds of the array” error in GenomeStudio, follow the troubleshooting steps below to identify and correct the underlying cause(s):

• Verify manifest and cluster file selection Ensure that the correct manifest and, if applicable, cluster files are being used. These files should match the Infinium BeadChip type and version associated with the dataset.

• Review the GenomeStudio log file Check the log file window located at the bottom of the GenomeStudio interface. This may provide additional details or identify a specific point of failure to guide troubleshooting.

• Exclude potential sample sheet issues Although this error is typically not related to the sample sheet, it can be helpful to create a project without a sample sheet to rule this out as a potential cause.

• Recreate the project using original IDAT files Attempt to create a new project directly from the IDAT files. If the files were received from a collaborator, obtain a new copy, as file corruption may occur during transfer.

• Re-download associated DMAPs and re-scan BeadChips Download a fresh copy of the DMAP files and re-scan the BeadChips to generate new IDAT files.

For any feedback or questions regarding this article (Illumina Knowledge Article #1901), contact Illumina Technical Support [e-mail].