what is the best time to do batch correction
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4 months ago
aimanbarki ▴ 20

I am working on scrna seq. I have 2 healthy sample and 4 stenosis human samples (NCBI). I have following questions and hoping someone can guide me on that.

  1. I upload each data set separately in R-seurat and do the quality check and remove the unwanted cells. Then merge the data (only 4 stenosis samples) in Seurat. Should I need to do batch correction before the dimension reduction or can I also do it after. I was thinking of merging the 4 stenosis sample together and perform the dimension reduction and then add the healthy samples? ( I have impression this is how its done on original paper … not sure)
  2. I am planning to run harmony on that. How can I select the batch correction method?
harmony batch correction • 137 views

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