SCTransform without integration #4862
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Chengwei94
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I answered this in a related question here: #5009 (comment) |
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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?
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