NOOB Background Correction

Correct methylation-array dye channels using out-of-band control means.

Description

Array-background correction separates estimated background from channel signal; this implementation uses mean subtraction.

Array-background correction separates estimated background from channel signal; this implementation uses mean subtraction.^[1]

Correct methylation-array dye channels using out-of-band control means.

When to use NOOB Background Correction

Use this tool to correct methylation-array dye channels using out-of-band control means.

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 NOOB Background Correction 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 redSignals, greenSignals, redOutOfBand, greenOutOfBand using the field table and calculation rules, then run the tool.
Read redCorrected, greenCorrected, redBackground, greenBackground. 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
redSignals	Red signals	list of number	Required
greenSignals	Green signals	list of number	Required
redOutOfBand	Red out of band	list of number	Required
greenOutOfBand	Green out of band	list of number	Required

Enter nonempty aligned red/green signals and separate nonempty control lists. Return mean backgrounds and clipped corrected arrays; entries must be finite.

corrected=max(0,signal−mean(outOfBandControls))

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

Output field	Meaning	Value type
redCorrected	Red corrected	list of number
greenCorrected	Green corrected	list of number
redBackground	Red background	number
greenBackground	Green background	number

json

{
  "input": {
    "redSignals": [
      10,
      20
    ],
    "greenSignals": [
      5,
      15
    ],
    "redOutOfBand": [
      2,
      4
    ],
    "greenOutOfBand": [
      1,
      3
    ]
  },
  "output": {
    "redCorrected": [
      7,
      17
    ],
    "greenCorrected": [
      3,
      13
    ],
    "redBackground": 3,
    "greenBackground": 2
  }
}

Limitations and assumptions

This is not full normal-exponential Noob or dye-bias normalization. Signed inputs are accepted.

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.

Alternative or Complementary methods

Use Single-CpG Methylation: Calculate single-CpG methylation after background correction. For a complementary task, use Input Background Correction: Subtract input background from epigenomic sample signals.

References

NOOB Background Correction — tool.io

Similar or alternative tools

Single-CpG Methylation
Calculate single-CpG methylation after background correction.
Input Background Correction
Subtract input background from epigenomic sample signals.