Batch correction methylation array datasets. any packages?
Dear all,
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.
Thanks
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I think that sva is your go-to in this case unless you think there is a specific effect for methylation that is more nuanced that will make a surrogate effect act differently on this data. Since you only have processed data I think you'll be good with that.
Can you suggest a command specific for methylation data?