Probe Pvalue Filter

Exclude methylation probes failing a detection p-value threshold.

Description

Detection p-values screen probe quality separately from biological differential-methylation tests.

Detection p-values screen probe quality separately from biological differential-methylation tests.^[1]

Exclude methylation probes failing a detection p-value threshold.

When to use Probe Pvalue Filter

Use this tool to exclude methylation probes failing a detection p-value threshold.

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 Probe Pvalue Filter 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 probePValues, maximumP using the field table and calculation rules, then run the tool.
Read retainedIndexes, failedIndexes, failurePercent. 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
probePValues	Probe p values	list of number	Required
maximumP	Maximum p	number	Required

Enter nonempty p-values and cutoff 0–1. Return passing zero-based indices and failure percentage.

pass=p≤cutoff

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

Output field	Meaning	Value type
retainedIndexes	Retained indexes	list of number
failedIndexes	Failed indexes	list of number
failurePercent	Failure percent	number

json

{
  "input": {
    "probePValues": [
      0.01,
      0.1,
      0.02
    ],
    "maximumP": 0.05
  },
  "output": {
    "retainedIndexes": [
      0,
      2
    ],
    "failedIndexes": [
      1
    ],
    "failurePercent": 33.33333333333333
  }
}

Limitations and assumptions

No p-values or multiple-testing adjustment are 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.

Alternative or Complementary methods

Use Probe Risk Filter: Filter probes against caller-supplied SNP-affected and cross-reactive ID lists. For a complementary task, use DMP Significance Gate: Gate single-CpG differential methylation by FDR and effect size.

References

Probe Pvalue Filter — tool.io

Similar or alternative tools

Probe Risk Filter
Filter probes against caller-supplied SNP-affected and cross-reactive ID lists.
DMP Significance Gate
Gate single-CpG differential methylation by FDR and effect size.