ComBat.mc {ENmix} | R Documentation |
A multi-processor wrapper for ComBat method. ComBat is a method to adjust batch effect where the batch covariate is known.
ComBat.mc(dat,batch,nCores = 1,...)
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 |
A data matrix with the same dimension as input data, adjusted for batch effects. Warning: Values for multimodal distributed CpGs could be over-adjusted.
Zongli Xu
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 ComBat
in sva
package for details.
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) }}