# TPM, FPKM and raw counts (expression units)

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

## TL;DR

Raw counts are how many sequencing reads hit each gene; TPM and FPKM rescale them for gene length and sequencing depth so genes and samples can be compared, and log2 TPM is the usual model input.

## Summary

RNA-Seq analysis quantifies expression from read counts per gene (Wikipedia); because longer genes and deeper libraries collect more reads, counts are normalised to fragments per kilobase per million (FPKM) or transcripts per million (TPM), which sum to a constant per sample. Quantifiers such as Salmon estimate transcript abundance and TPM directly. Models usually take log2(TPM + 1); mixing units, or mixing TPM from one pipeline with counts from another, is a classic source of batch effects.

## Fields

- Kind: Term
- Last checked: 2026-09-24
- Also known as: TPM; transcripts per million; FPKM; RPKM; log2 TPM; log2(TPM+1); raw counts; read counts; expression units
- 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/tpm-fpkm-counts.

## Sources

- Wikipedia: https://en.wikipedia.org/wiki/RNA-Seq
- Salmon: fast and bias-aware quantification of transcript expression (Nature Methods 2017): https://doi.org/10.1038/nmeth.4197
- Wikipedia: https://en.wikipedia.org/wiki/RNA-Seq

## Connected records

- terms: [Batch effects and harmonisation](https://onco.cc/terms/batch-effects/), [Bulk RNA sequencing (RNA-seq) and the full transcriptome](https://onco.cc/terms/bulk-rna-seq/), [Cancer AI vocabulary (CanSim terms map)](https://onco.cc/terms/cancer-ai-vocabulary/), [Quantile normalisation, rank transforms and z-scores](https://onco.cc/terms/quantile-normalisation/), [STAR and Salmon (RNA-seq alignment and quantification)](https://onco.cc/terms/star-salmon/), [Units of measurement ontology (UO)](https://onco.cc/terms/units-ontology/)

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JSON: https://onco.cc/api/v1/entities/tpm-fpkm-counts.json