combatbaaddon {bapred}R Documentation

Addon batch effect adjustment using ComBat


Performs addon batch effect adjustment using ComBat. Takes the output of performing combatba on a training data set and new batch data and correspondingly adjusts the test data to better match the adjusted training data according to the ComBat model


combatbaaddon(params, x, batch)



object of class combat. Contains parameters necessary for addon batch effect adjustment.


matrix. The covariate matrix of the new data. Observations in rows, variables in columns.


factor. Batch variable of the new data. Currently has to have levels: '1', '2', '3' and so on.


The adjusted covariate matrix of the test data.


The original ComBat-code is used in combatbaaddon: (Access date: 2015/06/19)


Roman Hornung


Johnson, W. E., Rabinovic, A., Li, C. (2007) Adjusting batch effects in microarray expression data using empirical bayes methods. Biostatistics, 8, 118-127.

Luo, J., Schumacher, M., Scherer, A., Sanoudou, D., Megherbi, D., Davison, T., Shi, T., Tong, W., Shi, L., Hong, H., Zhao, C., Elloumi, F., Shi, W., Thomas, R., Lin, S., Tillinghast, G., Liu, G., Zhou, Y., Herman, D., Li, Y., Deng, Y., Fang, H., Bushel, P., Woods, M., Zhang, J. (2010) A comparison of batch effect removal methods for enhancement of prediction performance using maqc-ii microarray gene expression data. The Pharmacogenomics Journal, 10, 278-291.



trainind <- which(batch %in% c(1,2))

Xtrain <- X[trainind,]
ytrain <- y[trainind]
batchtrain <- factor(as.numeric(batch[trainind]), levels=c(1,2))

testind <- which(batch %in% c(3,4))

Xtest <- X[testind,]
ytest <- y[testind]

batchtest <- as.numeric(batch[testind])
batchtest[batchtest==3] <- 1
batchtest[batchtest==4] <- 2
batchtest <- factor(batchtest, levels=c(1,2))

params <- combatba(x=Xtrain, batch=batchtrain)

Xtestaddon <- combatbaaddon(params, x=Xtest, batch=batchtest)

[Package bapred version 1.0 Index]