bio-differential-expression-batch-correction

ComBat-Seq (Count Data)

Goal: Remove batch effects from raw count data while preserving biological group differences.

Approach: Apply ComBat-Seq's negative binomial regression to adjust counts, keeping the integer nature of the data.

"Remove batch effects from my RNA-seq counts" → Adjust raw count matrix for known batch labels using negative binomial modeling, preserving biological condition effects.

library(sva)

## ComBat (Normalized Data)

**Goal:** Remove batch effects from normalized (log-transformed or TPM) expression data.

**Approach:** Apply parametric empirical Bayes adjustment to normalized expression while protecting biological covariates.

```r
library(sva)

## Run ComBat

corrected_expr <- ComBat(dat = as.matrix(normalized_expr),
                          batch = metadata$batch,
                          mod = mod,
                          par.prior = TRUE)