I’m working with libraries prepped via 10x and our samples are from two different tissue types. I’ve been asked to preemptively adjust for ambient RNA given that these two tissue types are quite different and ambient RNA contamination could skew our data.
I am using scVI for my differential expression analysis. Would it be advisable to use ambient RNA adjustment packages like scAR or Cellbender prior to scVI? Or would scVI be sufficient enough to correct for ambient RNA on its own?
Thank you in advance. I’m still in the early phases of my bioinformatics training.