Can anyone help me with batch correction for methylation array datasets?
I have data from different labs. Some are 850K and other are 450K. I don't have raw idat files for some samples so I cannot use champ.runcombat function..
I thought to use Combat from svg package but I prefer in-built functions of methylation array specific R packages. I applied BEClear but it does not work well.
Please suggest some R package to do that and share if anybody have prior experience.