Replicate Concordance

Calculate biological-replicate Pearson concordance and gate status.

Description

Pearson correlation measures linear association, which differs from replicate agreement.

Pearson correlation measures linear association, which differs from replicate agreement.^[1]

Calculate biological-replicate Pearson concordance and gate status.

When to use Replicate Concordance

Use this tool to calculate biological-replicate Pearson concordance and gate status.

Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.

How to use Replicate Concordance and understand its results

Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
Enter firstReplicate, secondReplicate, minimumCorrelation using the field table and calculation rules, then run the tool.
Read pearsonCorrelation, meanAbsoluteDifference, passesGate. 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
firstReplicate	First replicate values	list of number	Required
secondReplicate	Second replicate values	list of number	Required
minimumCorrelation	Minimum Pearson correlation	number; minimum: -1; maximum: 1	Required

Enter at least two aligned finite observations varying in both lists and minimum correlation. Return r, mean absolute difference and inclusive gate.

r=covarianceSum/sqrt(sumSquaredX×sumSquaredY)

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

Output field	Meaning	Value type
pearsonCorrelation	Pearson correlation	number; minimum: -1; maximum: 1
meanAbsoluteDifference	Mean absolute difference	number; minimum: 0
passesGate	Passes supplied concordance gate	boolean

json

{
  "input": {
    "firstReplicate": [
      1,
      2,
      3
    ],
    "secondReplicate": [
      2,
      4,
      6
    ],
    "minimumCorrelation": 0.9
  },
  "output": {
    "pearsonCorrelation": 1,
    "meanAbsoluteDifference": 2,
    "passesGate": true
  }
}

Limitations and assumptions

No agreement model, p-value or batch correction is calculated.

Numeric inputs, where present, 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. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use Spike-In Scaling: Apply a spike-in normalization factor to sample signals. For a complementary task, use IDR Consistency: Check replicate consistency from IDR values.

References

Replicate Concordance — tool.io

Similar or alternative tools

Spike-In Scaling
Apply a spike-in normalization factor to sample signals.
IDR Consistency
Check replicate consistency from IDR values.