# Quantile normalisation, rank transforms and z-scores

Source: https://onco.cc/terms/quantile-normalisation/  
OnCo record `quantile-normalisation` (Term). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

Quantile normalisation forces every sample's expression values onto the same distribution by rank, and a z-score expresses each gene as standard deviations from its mean; both are ways to make data from different platforms comparable.

## Summary

Quantile normalisation makes two distributions identical in statistical properties by sorting both and replacing each value with the reference value of the same rank (Wikipedia); it can be applied to a single new sample against a fixed reference, which makes it usable at prediction time. A standard score is the number of standard deviations a value lies from the mean (Wikipedia), applied per gene it aligns RNA-seq and microarray means but needs a cohort to estimate. Both are the correctness backbone that lets a TCGA model read a METABRIC sample.

## Fields

- Kind: Term
- Last checked: 2026-09-24
- Also known as: quantile normalisation; quantile normalization; QN; rank normalisation; rank transform; per-gene z-score; z-score normalisation; z-scoring; standard score
- Tags: cansim-terms

## Notes

- Listed in the CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme; CanSim page path /terms/quantile-normalisation.

## Sources

- Wikipedia: https://en.wikipedia.org/wiki/Quantile_normalization
- Wikipedia: standard score: https://en.wikipedia.org/wiki/Standard_score
- Wikipedia: https://en.wikipedia.org/wiki/Quantile_normalization

## Connected records

- terms: [Batch effects and harmonisation](https://onco.cc/terms/batch-effects/), [Cancer AI vocabulary (CanSim terms map)](https://onco.cc/terms/cancer-ai-vocabulary/), [Domain shift and domain adaptation (cell line to patient)](https://onco.cc/terms/domain-adaptation/), [Microarray expression data](https://onco.cc/terms/microarray-expression/), [TPM, FPKM and raw counts (expression units)](https://onco.cc/terms/tpm-fpkm-counts/)

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JSON: https://onco.cc/api/v1/entities/quantile-normalisation.json