{"entity":{"id":"tpm-fpkm-counts","kind":"term","name":"TPM, FPKM and raw counts (expression units)","aka":["TPM","transcripts per million","FPKM","RPKM","log2 TPM","log2(TPM+1)","raw counts","read counts","expression units"],"tldr":"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.","asOf":"2026-09-24","wikipedia":"https://en.wikipedia.org/wiki/RNA-Seq","links":[{"label":"Salmon: fast and bias-aware quantification of transcript expression (Nature Methods 2017)","url":"https://doi.org/10.1038/nmeth.4197"},{"label":"Wikipedia","url":"https://en.wikipedia.org/wiki/RNA-Seq"}],"tags":["cansim-terms"],"related":["cancer-ai-vocabulary"],"cancers":[],"sections":[],"technologies":[],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["bulk-rna-seq","batch-effects","quantile-normalisation"],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":[],"dependsOn":[],"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."],"provenance":{"editedBy":"OnCo CanSim terms wave (Wikipedia summaries, standards and project pages, GDC and FDA pages, Europe PMC)","editedOn":"2026-09-24","note":"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"},"category":"Genomics & genetics"},"route":"/terms/tpm-fpkm-counts/","neighbours":{"term":[{"id":"batch-effects","kind":"term","name":"Batch effects and harmonisation","route":"/terms/batch-effects/"},{"id":"bulk-rna-seq","kind":"term","name":"Bulk RNA sequencing (RNA-seq) and the full transcriptome","route":"/terms/bulk-rna-seq/"},{"id":"cancer-ai-vocabulary","kind":"term","name":"Cancer AI vocabulary (CanSim terms map)","route":"/terms/cancer-ai-vocabulary/"},{"id":"quantile-normalisation","kind":"term","name":"Quantile normalisation, rank transforms and z-scores","route":"/terms/quantile-normalisation/"},{"id":"star-salmon","kind":"term","name":"STAR and Salmon (RNA-seq alignment and quantification)","route":"/terms/star-salmon/"},{"id":"units-ontology","kind":"term","name":"Units of measurement ontology (UO)","route":"/terms/units-ontology/"}]}}