bapred (version 1.1)

ratioa: Batch effect adjustment using Ratio-A

Description

Performs batch effect adjustment using Ratio-A. Here, the variable values are divided by the batch-specific arithmetic mean of the corresponding variable.

Usage

ratioa(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

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

xadj

matrix of adjusted (training) data

nbatches

number of batches

batch

batch variable

References

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, <10.1038/tpj.2010.57>.

Examples

# NOT RUN {
data(autism)

params <- ratioa(x=X, batch=batch)
# }