How do I use muscat if my single cell data comes from different datasets with clear batch effects?

[WyzhaoJo]

My single cell data comes from different datasets. There are clear batch effects. How do I remove batch effects in pseudobulk analysis?Thanks a lot!

[plger]

Use the design argument:

mm <- model.matrix(~batch+group)
res <- pbDS(pb, design=mm)

If you have a complex design you might also want to use the contrast or coef argument of pbDS to specify what specific effect you want to test. If you need more info on that, google or check chapter 9 of limma::limmaUsersGuide().

[WyzhaoJo]

Thanks!!I'll try it tomorrow!!