Construct · 1 fields · 2 citations

batch: a standalone construct

One name. One construct. A landmark on the map.

● anchor · a standalone construct Nearest construct by meaningruncompare the meanings
How to read this

Every construct on the map is compared with every other by the meaning of its definitions, and the closest one is surfaced here. The nearest construct to batch is run.

Hold this as a prompt, not a verdict. Two constructs sitting close in meaning is a reason to read them side by side and decide for yourself whether they are one idea under two names. It is not proof that they are. Compare the meanings in the Collider.

batch1 CONSTRUCTBatch effectJOHNSON · BATCH EFFECT

A single standalone construct; nearby constructs are located against it in the Collider. Tap a field for its definition, unit, and measures.

Genomics and high-throughput measurement

A processing group and its technical bias

In genomics and other high-throughput measurement, a batch is a group of samples processed together, on the same day, machine, or reagent lot, and a batch effect is the systematic technical variation this shared processing introduces into the data. Johnson, Li, and Rabinovic's 2007 Adjusting batch effects in microarray expression data using empirical Bayes methods introduced the ComBat method to estimate and remove this variation, and Leek and colleagues' 2010 Tackling the widespread and critical impact of batch effects in high-throughput data showed how often it distorts biological conclusions. The referent is a nuisance grouping of measurements and the bias it carries, not a manufacturing run or a set of training examples.[1][2]

Unit
A group of samples sharing a processing run, and the technical bias attached to it
Recovery means
Not applicable
Measured by
Detected as variation associated with the processing group and removed by adjustment methods such as empirical Bayes correction

Next

Run it through the Collider, or take the citations with you.

See how batch sits against neighbouring constructs in the Collider, or export every reference on this page in one click.

Open in ColliderExport BibTeXReport this entry

Nearby constructs

gradient4 fields · 4 citationsjingle · one word, four constructssample3 fields · 3 citationsjingle · one word, three constructsvariance4 fields · 6 citationsjingle · one word, four constructs

References

  1. Johnson, W. E., Li, C., & Rabinovic, A. (2007). Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics, 8(1), 118–127. https://doi.org/10.1093/biostatistics/kxj037
  2. Leek, J. T., Scharpf, R. B., Bravo, H. C., Simcha, D., Langmead, B., Johnson, W. E., Geman, D., Baggerly, K., & Irizarry, R. A. (2010). Tackling the widespread and critical impact of batch effects in high-throughput data. Nature Reviews Genetics, 11(10), 733–739. https://doi.org/10.1038/nrg2825

Cited on this page?

Confirm your construct, or correct us.

If your work is cited behind one of these entries, you know better than we do whether we captured the meaning right. Confirm it, suggest an edit, or dispute it, and your name goes on the entry as an author who has checked it, linked to your ORCID.

Claim your construct