How to correct batch effects when using muscat?

[ChenyuZhang97]

Hi,
I am new to using muscat to analyze the single-cell RNA-seq data. My data came from individually sequenced samples. So, I would like to know if it is necessary to correct the batch effects and how?
Many thanks!

[HelenaLC]

Hm. Not sure I correctly understand the question/issue, but: Both sample-level (pseudobulk-based) and single cell-level (mixed models) approaches can account for sample-to-sample variability, granted an appropriate design/formula is provided. If, however, your batches are confounded with the experimental conditions under interrogation, all is lost. But if, as you say, samples were sequenced individually, this should not be the case.

[ChenyuZhang97]

Thanks!