Ma Plot Coordinates

Generate MA-plot log-ratio and mean-abundance coordinates.

Description

MA coordinates separate a log2 expression ratio M from mean log2 abundance A.

MA coordinates separate a log2 expression ratio M from mean log2 abundance A. Both depend on the supplied pseudocount near zero signals.^[1]

Generate MA-plot log-ratio and mean-abundance coordinates.

When to use Ma Plot Coordinates

Use this tool to generate MA-plot log-ratio and mean-abundance coordinates.

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 Ma Plot Coordinates 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 treatmentCounts, controlCounts, pseudocount using the field table and calculation rules, then run the tool.
Read mCoordinates, aCoordinates. 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
treatmentCounts	Treatment counts	list of number	Required
controlCounts	Control counts	list of number	Required
pseudocount	Pseudocount	number	Required

Enter aligned nonempty lists and a nonnegative pseudocount. Require both adjusted values to be positive, calculate M/A per feature and preserve feature order. Signed raw values can be accepted if their adjusted values remain positive.

M=log2((treatment+p)/(control+p)); A=[log2(treatment+p)+log2(control+p)]/2

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

Output field	Meaning	Value type
mCoordinates	M coordinates	list of number
aCoordinates	A coordinates	list of number

json

{
  "input": {
    "treatmentCounts": [
      8,
      2
    ],
    "controlCounts": [
      2,
      8
    ],
    "pseudocount": 0
  },
  "output": {
    "mCoordinates": [
      2,
      -2
    ],
    "aCoordinates": [
      2,
      2
    ]
  }
}

Limitations and assumptions

The tool returns numeric coordinates without drawing a plot, normalizing libraries or testing differences. A is a mean of logs, not the log of an arithmetic mean.

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 Volcano Quadrant: Classify volcano-plot features with supplied effect and FDR thresholds. For a complementary task, use Two Color Log Ratio: Compute log2 Cy5/Cy3 spot ratios with an optional pseudocount.

References

Ma Plot Coordinates — tool.io

Similar or alternative tools

Volcano Quadrant
Classify volcano-plot features with supplied effect and FDR thresholds.
Two Color Log Ratio
Compute log2 Cy5/Cy3 spot ratios with an optional pseudocount.