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immunogenomics / harmony

Fast, sensitive and accurate integration of single-cell data with Harmony
https://portals.broadinstitute.org/harmony/
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harmony for normalized scRNA-seq dataset #224

Closed martina811 closed 9 months ago

martina811 commented 9 months ago

Hello, I would like to integrate 2 single cell datasets, but one has the raw counts and the other one the normalized counts, is harmony suitable to integrate these two kind of datasets?

Thank you for your help.

pati-ni commented 9 months ago

You should definitely normalize the raw counts as you would normally (size factors, log). For the normalized data you should figure out whether there are already log normalized. If not you should perform that step, so that variance is not driven by expression level.

This will ensure that your PCs are properly computed which harmony will use for batch correction. FYI, by default Harmony does not work with the counts data.