Dye Swap Correlation

Correlate forward dye ratios with sign-reversed dye-swap replicates.

Description

A dye swap reverses the channel ratio's sign.

A dye swap reverses the channel ratio's sign. Concordance therefore compares a forward ratio profile with the negative of its reverse-dye profile.^[1]

Correlate forward dye ratios with sign-reversed dye-swap replicates.

When to use Dye Swap Correlation

Use this tool to correlate forward dye ratios with sign-reversed dye-swap replicates.

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 Dye Swap Correlation 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 forwardLogRatios, reverseLogRatios, minimumCorrelation using the field table and calculation rules, then run the tool.
Read correlation, concordant. 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
forwardLogRatios	Forward log ratios	list of number	Required
reverseLogRatios	Reverse log ratios	list of number	Required
minimumCorrelation	Minimum correlation	number	Required

Enter aligned profiles with at least two spots and finite minimum correlation. Center both, negate reverse centered values for covariance and divide by both profile norms. Both profiles must vary. Return correlation and an inclusive concordance flag.

correlation=Pearson(forwardLogRatios,−reverseLogRatios)

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

Output field	Meaning	Value type
correlation	Correlation	number
concordant	Concordant	boolean

json

{
  "input": {
    "forwardLogRatios": [
      1,
      2,
      3
    ],
    "reverseLogRatios": [
      -1,
      -2,
      -3
    ],
    "minimumCorrelation": 0.8
  },
  "output": {
    "correlation": 1,
    "concordant": true
  }
}

Limitations and assumptions

No dye-bias correction, significance test or replicate alignment is performed. The criterion is caller supplied and not restricted to −1 through 1; a high correlation does not exclude systematic offsets.

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. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use Two Color Log Ratio: Compute log2 Cy5/Cy3 spot ratios with an optional pseudocount. For a complementary task, use LOESS Intensity Normalization: Apply tricube local intensity-bias smoothing to log-ratio signals.

References

Dye Swap Correlation — tool.io

Similar or alternative tools

Two Color Log Ratio
Compute log2 Cy5/Cy3 spot ratios with an optional pseudocount.
LOESS Intensity Normalization
Apply tricube local intensity-bias smoothing to log-ratio signals.