SCTransform without integration

[Chengwei94]

If I merge 3 different datasets using the merge function(no integration), should I be doing SCTtransform before or after merging? This question is mainly for the DE analysis since that if I do integration, I would be conducting DE analysis on data which are SCTransformed individually before integrated.

Follow up question: Wouldnt wilcoxon test be very sensitive to batch effects, since it can be interpreted as testing the median of between 2 distributions. If so, whats the suggested test for DE analysis with datasets that are heavily batched?

[saketkc]

I answered this in a related question here: #5009 (comment)