Apply batch effect with “combat” in wgcna
I have 336 samples, with
two conditions of fibrosis and normal ,
and male and female genders ,
and Chinese, Indian, Malay , Caucasian , Bruneian, and not reported nationalities,
I want to apply the batch effect by combat to this study before doing WGCNA.
How do I use the following function?
For example, what should I define as a batch?
ComBat( dat, batch, mod = NULL, par.prior = TRUE, prior.plots = FALSE, mean.only = FALSE, ref.batch = NULL, BPPARAM = bpparam("SerialParam") )
Thank you for your help
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