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hemberg-lab / SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
http://bioconductor.org/packages/SC3
GNU General Public License v3.0
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Running SC3 in integrated data #109

Closed anemartinezlarrinaga2898 closed 1 year ago

anemartinezlarrinaga2898 commented 1 year ago

Hello!

I wanted to ask if someone has tried to run SC3 in integrated data?

Thanks!

mhemberg commented 1 year ago

When we developed SC3, none of the methods for batch integration existed, so it has not been thoroughly tested for this purpose. Many batch correction methods do not change the count matrix, but instead they operate on a latent space. Hence they are not really compatible with SC3 as it takes the count matrix as input. However, then ones that do modify the count matrix should in principle work well.