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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