Volcano Quadrant

Classify volcano-plot features with supplied effect and FDR thresholds.

Description

A volcano screen combines effect size with an already adjusted p-value.

A volcano screen combines effect size with an already adjusted p-value. Threshold classification differs from estimating effects or controlling false discoveries from raw p-values.^[1]

Classify volcano-plot features with supplied effect and FDR thresholds.

When to use Volcano Quadrant

Use this tool to classify volcano-plot features with supplied effect and FDR thresholds.

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 Volcano Quadrant 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 log2FoldChanges, adjustedPValues, minimumAbsoluteLog2Fc, maximumAdjustedP using the field table and calculation rules, then run the tool.
Read quadrants, upCount, downCount. 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
log2FoldChanges	Log 2 fold changes	list of number	Required
adjustedPValues	Adjusted p values	list of number	Required
minimumAbsoluteLog2Fc	Minimum absolute log 2 fc	number	Required
maximumAdjustedP	Maximum adjusted p	number	Required

Enter aligned nonempty log2 effects and adjusted p-values in 0–1, a nonnegative effect cutoff and p cutoff in 0–1. Significant positive effects are up; other significant effects are down. Return labels and up/down counts. With zero effect cutoff, a zero effect meeting the p cutoff is labeled down.

significant=(adjustedP≤maximumAdjustedP) AND (|log2FC|≥minimumAbsoluteLog2Fc)

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

Output field	Meaning	Value type
quadrants	Quadrants	list of string
upCount	Up count	number
downCount	Down count	number

json

{
  "input": {
    "log2FoldChanges": [
      2,
      -2,
      0.1
    ],
    "adjustedPValues": [
      0.01,
      0.01,
      0.5
    ],
    "minimumAbsoluteLog2Fc": 1,
    "maximumAdjustedP": 0.05
  },
  "output": {
    "quadrants": [
      "up",
      "down",
      "not-significant"
    ],
    "upCount": 1,
    "downCount": 1
  }
}

Limitations and assumptions

No p-values or multiplicity adjustment are calculated. Direction depends on the treatment/reference convention, and a threshold label does not establish biological significance.

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 Ma Plot Coordinates: Generate MA-plot log-ratio and mean-abundance coordinates. For a complementary task, use Wilcoxon Rank Sum: Calculate a two-group Wilcoxon rank-sum statistic with averaged tied ranks.

References

Volcano Quadrant — tool.io

Similar or alternative tools

Ma Plot Coordinates
Generate MA-plot log-ratio and mean-abundance coordinates.
Wilcoxon Rank Sum
Calculate a two-group Wilcoxon rank-sum statistic with averaged tied ranks.