> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/dragen-protein-quantification/counting-and-normalization/qc-summary.md).

# QC Summary

## QC Checks

There are a number of quality control checks that are applied on a plate and sample level. Refer to the metrics appendix page for a summary of all metrics.

* **Minimum SOMAmer Read Counts:** **Non-blank samples** with less than **10 million** reads will receive a **FLAG** for SOMAmerReads\_PassFlag in the ADAT. These reads are counted in the raw counts step. Only human protein SOMAmers are part of this count, not controls. There is no specification for blank samples.
* **Maximum SOMAmer Read Counts:\*\*\*\* Blank samples** with more than **20 million normalized reads** will receive a **FLAG** for SOMAmerNormRead\_PassFlag in the ADAT. These reads are counted in the plate scale normalization step. Only human protein SOMAmers are part of this count, not controls. There is no specification for non-blank samples. A **plate** where **70% of the blanks** have a **FLAG** for this step will receive a **WARNING**.
* **Reference Correlation:** This step produces a Spearman correlation coefficient describing how similar a sample is to a an external Plasma or Serum reference (see below). There is no pass flag for this step.
  * The reference used in this step can be found in the SOMAmer metadata, under Ref.MedNormExt.Plasma, Ref.MedNormExt.Serum, or Ref.MedNormExt.CSF (dependent on the input type).
* **HybQC:** The assay includes a set of built-in SOMAmer controls with known melting temperatures (Tms) spanning the full temperature range used in the assay. Under normal hybridization conditions, the counts from these controls follow a characteristic S-shaped (sigmoidal) pattern when plotted against their Tms. The HybQC metric captures the midpoint of this curve, where the transition from low to high signal occurs along the temperature axis. This midpoint is compared to a reference (HybQC\_Ref) When comparing each samples HybQC to the HybQC\_Delta, if **HybQC is greater than the Delta threshold**, the sample will receive a **FLAG**.
  * The reference and delta used in this step can be found in the ADAT header (HybQC\_Reference and HybQC\_Delta).
* **QC Check:** This step compares the median of each SOMAmer measurement, across the three QC sample replicates, to an external QC reference. It then calculates a SOMAmer-specific scale factor and a QC metric (QCCheckTailPercent). QCCheckTailPercent corresponds to the percentage of SOMAmers with scale factors outside the specification range (**0.8**–**1.2**). If more than **15%** of the scale factors are outside of the specification range, the plate receives a **FAIL**.
  * The references used in this step can be found in the SOMAmer metadata, under Ref.QCCheck.Plasma, Ref.QCCheck.Serum, or Ref.QCCheck.CSF (dependent on the input type).
  * MultiMatrix uses serum QC samples and their corresponding platform-specific external references for plate scaling and QC. Performed after platform-specific plate scaling, this QC step compares the median of each SOMAmer measurement, across the Serum QC replicates, to the external reference, calculates a SOMAmer-specific scale factor (PlatformSpecificQCCheck\_\<PlateBarcode>\_ScaleFactor), and computes a plate-level metric (PlatformSpecificQCCheckTailPercent). PlatformSpecificQCCheckTailPercent corresponds to the percentage of SOMAmers with scale factors outside the specification range (**0.4**-**1.6**). If more than **15%** of scale factors fall outside the specification range, the plate receives a **WARNING** for PlatformSpecificQCCheckTailPercent\_PassFlag.


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