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. Currently has to have levels: '1', '2', '3' and so on.
Value
combatba returns an object of class combat.
An object of class "combat" is a list containing the following components:
xadjmatrix of adjusted (training) data
meanoverallvector containing the overall means of the variables. Used in addon adjustment.
var.pooledvector containing the pooled variances of the variables. Used in addon adjustment.
batchbatch variable
nbatchesnumber of batches
References
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.