QC Reporting

[dmccloskey]

Description

Reports for feature and sequence QCs that are intended to indicate the relative quality of a particular feature or sample compared to others in the sequence. Feature QCs will be used to decide when a particular dilution should be used.

Objective

• [x] Single value summary statistic on a component and component_group quality that can be included in the SequenceSummary report
• [x] Single value summary statistic on a sample that could be included in a SampleReport
• [ ] Basic visualizations and plots
• [ ] Summary report of what the script did (i.e., samples and analytes analyzed)

Reports

• FeatureSummary: columns for sample_name, component_name, component_group_name, feature_name, samplename, used, component_flag, component_group_flag, component_quality_score, component_group_quality_score
• SequenceSummary: matrix of final component_names and sample_names

Visualizations

• metric plot for e.g., IS or calibrators
• box and whiskers plots for QCs
• box and whiskers plots for sample groups
• PCA plot for Unknowns

[dmccloskey]

Single value summary statistic on a component and component_group quality

Find examples of the following peaks in BloodProject_PLT_QC-1

• saturated peak (e.g., glu-L.Heavy)
• LLOD peak (e.g., g6p from -10x)
• perfect peak (e.g., camp)
• ugly peak (e.g., arg-L)
• tailing peak (e.g., dhap [high] atp [low])
• fronting peak (e.g.,pyr.pyr_1.Light)
• split peak (e.g., f6p)
• high baseline peak (e.g., akg)
• cutoff peak (e.g., adp_2.Light)
• noise (e.g., chor)

examples saved to DropBox

[dmccloskey]

component quality metric:

• 1/(n QC metrics)*binary(0 or 1 for pass or fail) + ...

component_group quality metric:

• 1/(n QC metrics)*binary(0 or 1 for pass or fail) + ...

[dmccloskey]

quality score experiment

transition level matrix:

• logSN and intensity
• peak shape metrics only
• logSN and intensity + peak shape metrics

transition group:

• n_transitions...
• sn_score, intensity_score
• n_transitions + sn_score, intensity_score

run quality:

• resolution between critical pairs
• average of all transition/group scores