Question: comparing ScRNA-seq data from two different studies: should batch effects be corrected with pooled cells or not?
gravatar for demoraesdiogo2017
6 months ago by
demoraesdiogo201740 wrote:

Hello I would like to compare T cells from this study with T cells from this study

However, I'm not sure if I should remove batch effects from each dataset separately or with both studies pooled, especially because each author used a different method.

Perhaps selecting the cells I want and performing a differential expression analysis would be better?

scrna-seq • 188 views
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