Batch adjustment by reference alignment (BARA): Improved prediction performance in biological test sets with batch effects

Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift


Many biological data acquisition platforms suffer from inadvertent inclusion of biologically irrelevant variance in analyzed data, collectively termed batch effects. Batch effects can lead to difficulties in downstream analysis by lowering the power to detect biologically interesting differences and can in certain instances lead to false discoveries. They are especially troublesome in predictive modelling where samples in training sets and test sets are often completely correlated with batches. In this article, we present BARA, a normalization method for adjusting batch effects in predictive modelling. BARA utilizes a few reference samples to adjust for batch effects in a compressed data space spanned by the training set. We evaluate BARA using a collection of publicly available datasets and three different prediction models, and compare its performance to already existing methods developed for similar purposes. The results show that data normalized with BARA generates high and consistent prediction performances. Further, they suggest that BARA produces reliable performances independent of the examined classifiers. We therefore conclude that BARA has great potential to facilitate the development of predictive assays where test sets and training sets are correlated with batch.


Enheter & grupper
Externa organisationer
  • SenzaGen AB

Ämnesklassifikation (UKÄ) – OBLIGATORISK

  • Bioinformatik (beräkningsbiologi)
TidskriftPLoS ONE
Utgåva nummer2
StatusPublished - 2019 feb 22
Peer review utfördJa

Relaterad forskningsoutput

Robin Gradin, 2020 nov 27, Department of Immunotechnology, Lund University. 123 s.

Forskningsoutput: AvhandlingDoktorsavhandling (sammanläggning)

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