Removing batch effects for prediction problems with frozen surrogate variable analysis.

TitleRemoving batch effects for prediction problems with frozen surrogate variable analysis.
Publication TypeJournal Article
AuthorsParker HS, Bravo HCorrada, Leek JT
2014
JournalPeerJ
Volume2
Pagese561

Batch effects are responsible for the failure of promising genomic prognostic signatures, major ambiguities in published genomic results, and retractions of widely-publicized findings. Batch effect corrections have been developed to remove these artifacts, but they are designed to be used in population studies. But genomic technologies are beginning to be used in clinical applications where samples are analyzed one at a time for diagnostic, prognostic, and predictive applications. There are currently no batch correction methods that have been developed specifically for prediction. In this paper, we propose an new method called frozen surrogate variable analysis (fSVA) that borrows strength from a training set for individual sample batch correction. We show that fSVA improves prediction accuracy in simulations and in public genomic studies. fSVA is available as part of the sva Bioconductor package.

10.7717/peerj.561
PubMed ID25332844
PubMed Central IDPMC4179553
Grant ListR01 GM083084 / GM / NIGMS NIH HHS / United States