Batch Effect Correction

ComBat-Seq (Count Data)

library(sva)

# counts: raw count matrix (genes x samples)
# batch: vector of batch labels
# group: vector of biological condition (optional, to preserve)

corrected_counts <- ComBat_seq(counts = as.matrix(counts),
                                batch = batch,
                                group = condition,
                                full_mod = TRUE)

# Result is batch-corrected count matrix
# Use for visualization, clustering, but NOT for DE (use design formula instead)