batchtma: batchtma: Methods to address batch effects

Description Functions References See Also


The goal of the batchtma is to provide functions for batch effect-adjusting biomarker data. It implements different methods that address batch effects while retaining differences between batches that may be due to “true” underlying differences in factors that drive biomarker values (confounders).


adjust_batch: Adjust for batch effects

diagnose_models: Model diagnostics after batch adjustment

plot_batch: Plot biomarkers by batch


Stopsack KH, Tyekucheva S, Wang M, Gerke TA, Vaselkiv JB, Penney KL, Kantoff PW, Finn SP, Fiorentino M, Loda M, Lotan TL, Parmigiani G+, Mucci LA+ (+ equal contribution). Extent, impact, and mitigation of batch effects in tumor biomarker studies using tissue microarrays. bioRxiv 2021.06.29.450369; doi:

See Also

batchtma documentation built on Dec. 6, 2021, 9:09 a.m.