Handling batch effects

[WJRDW]

Hi EcoTyper team,

Thank you for the amazing tool!
I'm running de novo discovery of cell states and ecotypes on a large cohort of bulk RNA-seq tumor samples coming from different datasets.
I was wondering how to handle batch effects best for this kind of cohort. Should I first try to correct for batch effects by for example using ComBat and run EcoTyper on the batch-corrected expression values or is it more advisable to include this batch variable in EcoTyper directly by specifying it in 'Annotation file column to scale by'.

Any suggestions would be very welcome!
Thank you very much in advance.

Best,
W

[KOBE24DUNK]

With the same question, and I look forward to hearing some suggestions.
Many thanks!