ComBat.mc {ENmix} | R Documentation

## A multi-processor wrapper for ComBat method.

### Description

A multi-processor wrapper for ComBat method. ComBat is a method to adjust batch effect where the batch covariate is known.

### Usage

    ComBat.mc(dat,batch,nCores = 1,...)

### Arguments

`dat` | A data matrix with column for samples and row for probe.
`batch` | Batch covariate (multiple batches allowed)
`nCores` | Number of cores will be used for computation
`...` | See `ComBat` in `sva` package for extra options

### Value

A data matrix with the same dimension as input data, adjusted for batch effects. Warning: Values for multimodal distributed CpGs could be over-adjusted.

### Author(s)

Zongli Xu

### References

Johnson, WE, Rabinovic, A, and Li, C (2007). Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics 8(1):118-127.

### See Also

See `ComBat` in `sva` package for details.

### Examples

    if(FALSE){
    if (require(minfiData)) {
    mdat=preprocessENmix(RGsetEx,bgParaEst="oob",nCores=6)
    mdat=norm.quantile(mdat,method="quantile1")
    beta=bmiq.mc(mdat,nCores=10)
    batch=factor(pData(mdat)$Slide)
    betaC=ComBat.mc(beta,batch,nCores=6,mod=NULL)
    }}

[Package ENmix version 1.21.6 Index]