Input Background Correction

Subtract input background from epigenomic sample signals.

Description

Input subtraction removes a supplied background while preserving signed residuals.

Input subtraction removes a supplied background while preserving signed residuals.^[1]

Subtract input background from epigenomic sample signals.

When to use Input Background Correction

Use this tool to subtract input background from epigenomic sample signals.

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 Input 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 sampleSignals, inputSignals using the field table and calculation rules, then run the tool.
Read correctedSignals, correctedSignalTotal, negativeCorrectedCount. 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
sampleSignals	Sample signals	list of number	Required
inputSignals	Input background signals	list of number	Required

Enter nonempty aligned finite lists; return corrected values, sum and negative count.

corrected[i]=signal[i]−background[i]

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

Output field	Meaning	Value type
correctedSignals	Input-subtracted signals	list of number
correctedSignalTotal	Corrected signal total	number
negativeCorrectedCount	Negative corrected values	integer; minimum: 0

json

{
  "input": {
    "sampleSignals": [
      10,
      20,
      5
    ],
    "inputSignals": [
      2,
      8,
      7
    ]
  },
  "output": {
    "correctedSignals": [
      8,
      12,
      -2
    ],
    "correctedSignalTotal": 18,
    "negativeCorrectedCount": 1
  }
}

Limitations and assumptions

No clipping, scaling or background estimation is performed.

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 NOOB Background Correction: Correct methylation-array dye channels using out-of-band control means. For a complementary task, use Spike-In Scaling: Apply a spike-in normalization factor to sample signals.

References

Input Background Correction — tool.io

Similar or alternative tools

NOOB Background Correction
Correct methylation-array dye channels using out-of-band control means.
Spike-In Scaling
Apply a spike-in normalization factor to sample signals.