batchtma: batchtma: Methods to address batch effects

In batchtma: Batch Effect Adjustments

Description

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).

Functions

adjust_batch: Adjust for batch effects

diagnose_models: Model diagnostics after batch adjustment

plot_batch: Plot biomarkers by batch

References

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: https://doi.org/10.1101/2021.06.29.450369

See Also

https://stopsack.github.io/batchtma/

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