{"entity":{"id":"batch-effects","kind":"term","name":"Batch effects and harmonisation","aka":["batch effects","batch effect","batch correction","ComBat","platform effect","cross-platform harmonisation","harmonisation across platforms"],"tldr":"A batch effect is a difference in the data caused by when, where or how samples were processed rather than by biology; if it lines up with the outcome, a model learns the batch instead of the disease.","summary":"In molecular biology a batch effect occurs when non-biological factors cause changes in the data, and it leads to wrong conclusions when its causes correlate with the outcome of interest (Wikipedia). Moving between RNA-seq and microarray, or between TCGA and a hospital cohort, is the extreme case. ComBat, from Johnson, Li and Rabinovic, is the standard empirical Bayes correction; per-gene z-scoring, quantile normalisation and rank transforms are the alternatives that need no batch labels. Any correction fitted on test data leaks.","asOf":"2026-09-24","wikipedia":"https://en.wikipedia.org/wiki/Batch_effect","links":[{"label":"Johnson, Li and Rabinovic, Adjusting batch effects in microarray expression data using empirical Bayes methods (ComBat, Biostatistics 2007)","url":"https://doi.org/10.1093/biostatistics/kxj037"},{"label":"sva Bioconductor package (ComBat)","url":"https://bioconductor.org/packages/release/bioc/html/sva.html"},{"label":"Wikipedia","url":"https://en.wikipedia.org/wiki/Batch_effect"}],"tags":["cansim-terms"],"related":["cancer-ai-vocabulary"],"cancers":[],"sections":[],"technologies":[],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["quantile-normalisation","tpm-fpkm-counts","microarray-expression","data-leakage"],"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/batch-effects."],"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/batch-effects/","neighbours":{"term":[{"id":"cancer-ai-vocabulary","kind":"term","name":"Cancer AI vocabulary (CanSim terms map)","route":"/terms/cancer-ai-vocabulary/"},{"id":"data-leakage","kind":"term","name":"Data leakage in model evaluation","route":"/terms/data-leakage/"},{"id":"domain-adaptation","kind":"term","name":"Domain shift and domain adaptation (cell line to patient)","route":"/terms/domain-adaptation/"},{"id":"magnification","kind":"term","name":"Magnification (20x, 40x) and microns per pixel","route":"/terms/magnification/"},{"id":"microarray-expression","kind":"term","name":"Microarray expression data","route":"/terms/microarray-expression/"},{"id":"quantile-normalisation","kind":"term","name":"Quantile normalisation, rank transforms and z-scores","route":"/terms/quantile-normalisation/"},{"id":"tpm-fpkm-counts","kind":"term","name":"TPM, FPKM and raw counts (expression units)","route":"/terms/tpm-fpkm-counts/"}]}}