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