Microarray Background Correction

Subtract local microarray background for each probe spot.

Description

Local background subtraction separates measured foreground signal from a supplied background estimate.

Local background subtraction separates measured foreground signal from a supplied background estimate. Negative corrected values may be useful diagnostic information rather than an automatic error.^[1]

Subtract local microarray background for each probe spot.

When to use Microarray Background Correction

Use this tool to subtract local microarray background for each probe spot.

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 Microarray Background Correction 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 foreground, localBackground, floorAtZero using the field table and calculation rules, then run the tool.
Read correctedSignals, backgroundTotal. 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
foreground	Foreground	list of number	Required
localBackground	Local background	list of number	Required
floorAtZero	Floor at zero	boolean	Required

Enter aligned nonempty finite foreground and nonnegative background lists and explicitly choose floorAtZero. Subtract each background, optionally clamp negatives and return corrected signals plus total supplied background. Raw foreground itself may be negative.

corrected_i=foreground_i−background_i; optionally max(0,corrected_i)

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

Output field	Meaning	Value type
correctedSignals	Corrected signals	list of number
backgroundTotal	Background total	number

json

{
  "input": {
    "foreground": [
      10,
      5,
      20
    ],
    "localBackground": [
      2,
      6,
      8
    ],
    "floorAtZero": true
  },
  "output": {
    "correctedSignals": [
      8,
      0,
      12
    ],
    "backgroundTotal": 16
  }
}

Limitations and assumptions

No background estimation, scanner calibration, spatial correction or normalization is performed. Clamping changes low-signal distributions and is a caller-selected behavior.

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 Two Color Log Ratio: Compute log2 Cy5/Cy3 spot ratios with an optional pseudocount. For a complementary task, use Quantile Normalization: Quantile-normalize multiple arrays, averaging tied-rank assignments.

References

Microarray Background Correction — tool.io

Similar or alternative tools

Two Color Log Ratio
Compute log2 Cy5/Cy3 spot ratios with an optional pseudocount.
Quantile Normalization
Quantile-normalize multiple arrays, averaging tied-rank assignments.