Batch effects are removed using the means of the batches.
1  mean_centering(Y, b)

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. 
A matrix of adjusted data with n rows and g columns.
Marco Giordan
ber
, ber_bg
, combat_np
, combat_p
, standardization
1 2 3 
Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.
All documentation is copyright its authors; we didn't write any of that.