combatba {bapred}

Batch effect adjustment using ComBat

Description

Performs batch effect adjustment using the parametric version of ComBat and additionally returns information necessary for addon batch effect adjustment with ComBat.

Usage

combatba(x, batch)

Arguments

x

matrix. The covariate matrix. Observations in rows, variables in columns.

batch

factor. Batch variable. Each factor level (or 'category') corresponds to one of the batches. For example, if there are four batches, this variable would have four factor levels and observations with the same factor level would belong to the same batch.

Value

combatba returns an object of class combat. An object of class "combat" is a list containing the following components:

xadj

matrix of adjusted (training) data

meanoverall

vector containing the overall means of the variables. Used in addon adjustment.

var.pooled

vector containing the pooled variances of the variables. Used in addon adjustment.

batch

batch variable

nbatches

number of batches

Note

The original ComBat-code is used in combatba: http://www.bu.edu/jlab/wp-assets/ComBat/Download.html (Access date: 2015/06/19)

Author(s)

Roman Hornung

References

Johnson, W. E., Rabinovic, A., Li, C. (2007). Adjusting batch effects in microarray expression data using empirical bayes methods. Biostatistics 8:118-127, <doi: 10.1093/biostatistics/kxj037>.

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, <doi: 10.1038/tpj.2010.57>.

Examples

data(autism)

combatba(x=X, batch=batch)