Expression Zscore

Map standardized expression to a clipped diverging-color coordinate.

Description

A z-score places expression relative to a supplied mean and SD.

A z-score places expression relative to a supplied mean and SD. A clipped color coordinate can summarize that score visually while preserving the unbounded numeric score separately.^[1]

Map standardized expression to a clipped diverging-color coordinate.

When to use Expression Zscore

Use this tool to map standardized expression to a clipped diverging-color coordinate.

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 Expression Zscore 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 expression, referenceMean, referenceStdDev, colorClipZ using the field table and calculation rules, then run the tool.
Read zScore, colorPosition. 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
expression	Expression	number	Required
referenceMean	Reference mean	number	Required
referenceStdDev	Reference std dev	number	Required
colorClipZ	Color clip z	number	Required

Enter finite expression/mean with positive reference SD and clipping threshold. Return the z-score and a color position between −1 and 1. Values beyond the chosen limits saturate only the color coordinate.

z=(expression−referenceMean)/referenceSD; color=max(−1,min(1,z/colorClipZ))

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

Output field	Meaning	Value type
zScore	Z score	number
colorPosition	Color position	number

json

{
  "input": {
    "expression": 8,
    "referenceMean": 5,
    "referenceStdDev": 2,
    "colorClipZ": 1
  },
  "output": {
    "zScore": 1.5,
    "colorPosition": 1
  }
}

Limitations and assumptions

Reference statistics are not estimated and no palette is rendered. Z-score interpretation depends on the chosen population and expression transformation; clipping hides magnitude differences in color.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Immune Signature Score: Score immune-cell signature enrichment from standardized gene expression. For a complementary task, use PCA Outlier Screen: Flag PCA samples outside a caller-selected radius.

References

Expression Zscore — tool.io

Similar or alternative tools

Immune Signature Score
Score immune-cell signature enrichment from standardized gene expression.
PCA Outlier Screen
Flag PCA samples outside a caller-selected radius.