This function performs batch correction on the variance-stabilized transformed data using the Limma package.
It can help identify potential batch effects or outliers.
Usage
run_batch_correction(
dds,
method = "limma",
batch,
save_data = TRUE,
save_dir = getwd()
)
Arguments
- dds
A DESeq2 object containing the normalized gene expression data
- method
Method to use for batch correction. Default is "limma".
- batch
Column name in colData(vsd) to use for batch correction.
- save_dir
Directory to save the results. Default is the current working directory
Value
A DESeq2 object containing the batch-corrected data