Matlab code for some popular batch correction methods.
Code available:
1.ComBat: bioconductor-sva-ComBat
Reference: W.E. Johnson, C. Li, and A. Rabinovic. Adjusting batch effects in microarray data using empirical bayes methods. Biostatistics, 8(1):118–127, 2007.
2.sva (surrogate variable analysis): bioconductor-sva package
Reference:
J.T. Leek and J.D. Storey. Capturing heterogeneity in gene expression studies by ‘surrogate variable analysis’. PLoS Genetics 3:e161, 2007.
J.T. Leek and J.D. Storey. A general framework for multiple testing dependence. Proceedings of the National Academy of Sciences 105:18718-18723, 2008