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Batch Effect

Definition
AI-generated

A batch effect is systematic technical variation associated with processing groups such as plates, centers, reagent lots, or genotyping waves rather than biology.

Topics
Epidemiology
Related
Bias Quality Control (QC) Variant Missingness

Why it matters in GWAS

If batch is correlated with case-control status or other traits, it can create spurious associations and distort QC metrics.

Example usage

"Principal components correlated with sequencing center, indicating a batch effect that we corrected before association testing."

Bias Quality Control (QC) Variant Missingness
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Anderson CA, et al. (2010). Data quality control in genetic case-control association studies. Nat Protoc.
← Batch Bayes factor →

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