Metrics Appendix

Sample Level Metrics

Sample level metrics are found in the sample/row-level metadata in the ADAT.

Metric
ADAT Field
Applied To
Threshold
Impact to Sample

Minimum SOMAmer Read Count

SOMAmerReads; SOMAmerReads_PassFlag

Non-Blank Samples

SOMAmerReads > 10 million

PASS/FLAG

Maximum SOMAmer Normalized Read Count

SOMAmerNormReads; SOMAmerNormReads_PassFlag

Blank Samples

SOMAmerNormReads < 40 million reads

PASS/FLAG

Hybridization Normalization

HybNorm_1_ScaleFactor; HybNorm_PassFlag

Non-Blank Samples

0.4 ≤ HybNorm_1_ScaleFactor ≤ 2.5

PASS/FLAG

Internal Reference Median Normalization

MedNormInt_5e-05_ScaleFactor; MedNormInt_0.005_ScaleFactor; MedNormInt_0.2_ScaleFactor; MedNormInt_PassFlag

Individual Blank and Calibrator samples, split by dilution group

0.4 ≤ MedNormInt_5e-05_ScaleFactor ≤ 2.5 0.4 ≤ MedNormInt_0.005_ScaleFactor ≤ 2.5 0.4 ≤ MedNormInt_0.2_ScaleFactor ≤ 2.5

PASS/FLAG

External Reference Median Normalization

MedNormExt_5e-05_ScaleFactor; MedNormExt_0.005_ScaleFactor; MedNormExt_0.2_ScaleFactor; MedNormExt_PassFlag

Individual non-control and QC samples, split by dilution group

0.4 ≤ MedNormExt_5e-05_ScaleFactor ≤ 2.5 0.4 ≤ MedNormExt_0.005_ScaleFactor ≤ 2.5 0.4 ≤ MedNormExt_0.2_ScaleFactor ≤ 2.5

PASS/FLAG

Correlation with Reference

RefCorr; RefCorr_PassFlag

Blank Samples

RefCorr < 0.6

PASS/FLAG

TM Controls

EmpiricalHybTemp

All samples

N/A

N/A

Row Check

RowCheck_PassFlag

All samples

The row check shall be PASS is all Pass Flags in this row are PASS; otherwise it shall be FLAG

PASS/FLAG

SOMAmer Level Metrics

SOMAmer level metrics are found in the SOMAmer/column-level metadata in the ADAT.

These PASS/FAIL designations are only used for plate level quality control. They should not be used to assess SOMAmer quality.

Metric
ADAT Field
Threshold
Impact to SOMAmer

Platform Specific Calibration

PlatformSpecificCalibrate_<PlateBarcode>_ScaleFactor; PlatformSpecificCalibrate_<PlateBarcode>_PassFlag

0.6 < PlatformSpecificCalibrate_<PlateBarcode>_ScaleFactor < 1.4

PASS/FAIL

Cross Platform Calibration

CrossPlatformCalibrate_<PlateBarcode>ScaleFactor;

CrossPlatformCalibrate<PlateBarcode>_PassFlag

0.6 < PCrossPlatformCalibrate_<PlateBarcode>_ScaleFactor < 1.4

PASS/FAIL

QC Check

QCCheck_<PlateBarcode>ScaleFactor; QCCheck_<PlateBarcode>_PassFlag

0.8 < QCCheck_<PlateBarcode>ScaleFactor < 1.2

PASS/FAIL

Plate Level Metrics

Plate level metrics are found in the header metadata in the ADAT.

Metric
ADAT Field
Threshold
Impact to Plate

QC Percent in Tails

QCCheckTailPercent; QCCheckTailPercent_PassFlag

QCCheckTailPercent < 15%

PASS/FAIL

Calibration Percent in Tails

PlatformSpecificCalibrateTailPercent; PlatformSpecificCalibrateTailPercent_PassFlag

PlatformSpecificCalibrateTailPercent < 15%

PASS/WARNING

SOMAmer Normalized Reads

PlateSOMAmerNormReads_PassFlag

< 70% of blank samples flagged at SOMAmerNormReads

PASS/WARNING

Reference Correlation

PlateRefCorr_PassFlag

< 70% of blank samples flagged at RefCorr

PASS/WARNING

Platform Specific Plate Scale

PlatformSpecificPlateScale_ScaleFactor

N/A

N/A

Cross Platform Plate Scale

CrossPlatformPlateScale_ScaleFactor

N/A

N/A

Cross Platform Calibration

CrossPlatformCalibrationTailPercent

N/A

N/A

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