Description Usage Arguments Details Value Author(s) References See Also Examples
Batch effects are removed using a two-stage regression approach and bagging.
1 |
Y |
A matrix with n rows and g columns, where n is the number of objects and g is the number of variables. In the case of gene expression data, columns correspond to genes (probe sets) and rows to samples. |
b |
A vector of class factor with the element in position i (i=1,…,n) representing the batch from which observation i belongs to. |
covariates |
An object of class data.frame where each column corresponds to a quantitative variable (of class numeric) or a qualitative variable (of class factor). |
partial |
A logical value indicating if partial bagging or full bugging have to be performed. See reference below. |
nSim |
Number of bootstrap samples. |
In this implementation NA values are not allowed.
A matrix of adjusted data with n rows and g columns.
Marco Giordan
M. Giordan. February 2013. A Two-Stage Procedure for the Removal of Batch Effects in Microarray Studies. Statistics in Biosciences.
ber
, combat_np
, combat_p
, mean_centering
, standardization
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