# QC Summary

## QC Checks

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

* <mark style="color:blue;">**Minimum SOMAmer Read Counts:**</mark> **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.
* <mark style="color:blue;">**Maximum SOMAmer Read Counts:**</mark>**&#x20;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**.
* <mark style="color:blue;">**Reference Correlation:**</mark> 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.QC or Ref.MedNormExt.Serum.QC (dependent on the input type).
* <mark style="color:blue;">**Empirical Hyb Temp:**</mark> This step uses 78 SOMAmer controls with a wide spectrum of melting temperature (Tm) from 28C to 72C, which represent the Tm of all probes used in the analysis. They were spiked to each sample at equal concentration; Tm controls with higher Tm have higher counts than those with lower Tm because their hybridization is more stable. The distribution of all Tm controls in a sample follows a logistic distribution; the inflection point is the EmpiricalHybTemp. This distribution is calculated using raw counts.
* <mark style="color:blue;">**QC Check:**</mark> 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 or Ref.QCCheck.Serum (dependent on the input type).