Applying BERMUDA to bulk RNA seq

[mdanb]

I have a relatively large bulk RNA seq dataset (~ 1300 samples, from ~70 experiments) that I'd like to correct for significant batch effects. Is it valid/possible to apply BERMUDA to my dataset? Instead of clustering cells of patients, I'd just cluster patients to remove batch effects. Is this valid?

[txWang]

While the use of domain adaptation in BERMUDA does not specifically restrict to single-cell data, the whole workflow of BERMUDA also depends on Seurat and Metaneighbor, which are designed for single-cell data. We also only applied BERMUDA in single-cell data in our paper. Therefore, I would suggest using the batch correction method designed for bulk data for your dataset.