I am working with an integrated SCTransformed dataset in Seurat v5. I have 2 different conditions inside the integrated object, and I now want to perform a pseudobulk DE analysis to see the effect of the treatment. I know that several people have tried to address this question (for example, https://github.com/satijalab/seurat/discussions/4032), but I am still confused. As far as I understand, I have to use the assay = "RNA". Great. What about the slot? Is it the "data" (thus the logNormalised one) or the "counts" (thus the raw data one) that needs to be used?
Also, for the visualisation purpose only (e.g. violin plots), is the data slot from the RNA assay the right one to be used or is the data slot from the SCT assay the right one?
Thank you to whoever can give me a clear answer!
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_deb •
1 answer
If you are doing pseudobulk, using for example DESeq2, the package requires raw counts, so slot="counts".
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this could be helpful: https://github.com/neurorestore/Libra