Why $SCT assay during differential expression analysis?
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Hello there!
I have a question regarding data integration using SCTransform.
The integration paper states that the $integrated assay data can be used for downstream analysis such as dimensionality reduction and clustering. Intuitively, I feel that for differential expression analysis, we should use the data with batch effect removed using anchors ($integrated). However, in the tutorial, it mentions using the data from $SCT assay for visualization and differential expression analysis.
I would like to know if there are any specific reasons to use the $SCT assay data. I did come across a previous issue suggesting the use of $SCT, but it did not mention the reasons behind it. Or, if there is any existing paper that addresses this, please let me know.
Sincerely,
Ryuzaman
It is covered on multiple issues on the seurat repo:
Thanks!