Apply a batch effect with "combatseq" in wgcna
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6 weeks ago
Maryam • 0

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. and I use DESeq2 for normalization data

How do I use the following function? I'm very confused to use scripts and I can't set scripts for my data For example, what should I define as a batch? and how set counts in this script

ComBat_seq(
counts,
batch,
group = NULL,
covar_mod = NULL,
full_mod = TRUE,
shrink = FALSE,
shrink.disp = FALSE,
gene.subset.n = NULL
)

count_matrix <- matrix(rnbinom(400, size=10, prob=0.1), nrow=50, ncol=8)
batch <- c(rep(1, 4), rep(2, 4))



deseq2 R batch combatseq wgcna • 416 views