MIQE Coverage Audit

Audit caller-supplied MIQE reporting checklist coverage.

Description

MIQE reporting guidance helps readers assess quantitative PCR experiments.

MIQE reporting guidance helps readers assess quantitative PCR experiments. Checklist coverage measures whether caller-defined item labels are present, not whether the reported evidence is adequate.^{[1, 2]}

Audit caller-supplied MIQE reporting checklist coverage.

When to use MIQE Coverage Audit

Use this tool to audit caller-supplied MIQE reporting checklist coverage.

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.

How to use MIQE Coverage Audit and understand its results

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
Enter requiredItems, documentedItems using the field table and calculation rules, then run the tool.
Read matchedItems, missingItems, coveragePercent. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
requiredItems	Required items	list of string	Required
documentedItems	Documented items	list of string	Required

Enter required and documented item lists. Trim and lowercase every label and deduplicate required items in first-occurrence order. Reject an empty required set or blank required label. Return normalized matched/missing labels and coverage percentage; documented duplicates do not increase coverage.

coverage%=100 matchedUniqueRequired/uniqueRequired

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
matchedItems	Matched items	list of string
missingItems	Missing items	list of string
coveragePercent	Coverage percent	number

json

{
  "input": {
    "requiredItems": [
      "primer-efficiency",
      "ntc",
      "replicates"
    ],
    "documentedItems": [
      "replicates",
      "ntc"
    ]
  },
  "output": {
    "matchedItems": [
      "ntc",
      "replicates"
    ],
    "missingItems": [
      "primer-efficiency"
    ],
    "coveragePercent": 66.66666666666666
  }
}

Limitations and assumptions

No checklist version is embedded, so supply the applicable reporting requirements explicitly. The tool does not read a manuscript, verify experimental quality or certify MIQE compliance.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use NTC Contamination Gate: Flag early no-template-control amplification against caller-supplied Ct limits. For a complementary task, use Bestkeeper Stability: Screen reference-gene Ct stability by replicate standard deviation.

Further background: MIQE 2.0: quantitative real-time PCR reporting guidance.

References

MIQE Coverage Audit — tool.io
MIQE 2.0: quantitative real-time PCR reporting guidance — Bustin et al., Clinical Chemistry

Similar or alternative tools

NTC Contamination Gate
Flag early no-template-control amplification against caller-supplied Ct limits.
Bestkeeper Stability
Screen reference-gene Ct stability by replicate standard deviation.