QC for IDATs uploaded from an iScan to Illumina BioInsight Platform Core for Microarray Analysis

IDAT files can be uploaded to Illumina BioInsight Platform Core (Platform Core, formerly, Illumina Connected Analytics (ICA)) automatically from the iScan or manually by selecting the files within Platform Core. Files uploaded from the iScan undergo quality checks (QC); whereas, manually uploaded files do not.###

Scanner Upload

Quality checks are performed for all sample data uploaded from the iScan to Platform Core. A status is assigned before files are sent to the cloud by the scanner. All files are uploaded regardless of QC status.

• QC criteria for IDATs

  • The scanner checks and validates per section metrics against the thresholds defined in .scst file that has been designated for the particular scan - Possible status assignments: Success, Failed, or Warning. Samples with a Fail status are unavailable for selection in BaseSpace Sequence Hub (BSSH).

  • To view the threshold values embedded in a given scan settings file, open the scan settings file from within the iScan Control Software (ICS). - From the main menu, select Tools=>Options

    Figure 1. Selecting Options from main menu - Select the Tab Scan Settings. A table listing the available Scan Settings Files will show. - Select a Scan Setting of interest, and the parameters for that Scan Setting will appear on the right. The QC parameters fall under the heading Grading.

    Figure 2. Scan Settings parameters for Infinium LCG

  • Minimum Registration score threshold for all Infinium scan settings is 0.75. See iScan Scan Metrics page for more details. - Samples with low registration score fail QC. - A sample could fail QC if one stripe has a low registration score even if all other stripes pass registration.

  • Thresholds for other grading parameters (Focus Quality, Percentile 05 Bead Intensity, Percentile 95 Bead Intensity, and Saturation) are set to very broad values and almost never fail, so that in general, only the Registration check would have impact on QC result.

• QC results are taken into consideration when launching Microarray analysis on BSSH.

  • Samples may be uploaded to Platform Core but are filtered out from selection if they fail instrument QC.

  • Poor performing samples are hidden from the user and not available for analysis.

Manual Upload

No QC checks are done when samples are uploaded manually.

• All manually uploaded samples are assigned a Passing instrument QC status and are available for analysis, regardless of the actual data quality.

References:

• Configuring iScan Control Software for Microarray data analysis on Illumina BioInsight Platform Core

• iScan System Product Documentation > Configure iScan Control Software > Use Illumina BioInsight Platform Core with the iScan System

For any feedback or questions regarding this article (Illumina Knowledge Article #10003), contact Illumina Technical Support [e-mail].