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SingleR-inc / SingleR

Clone of the Bioconductor repository for the SingleR package.
https://bioconductor.org/packages/devel/bioc/html/SingleR.html
GNU General Public License v3.0
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About non-corrected assay RNA assay counts slot generated by seurat integrated workflow using for old singler version to annotate cell issues #128

Closed honghh2018 closed 4 years ago

honghh2018 commented 4 years ago

Hi Developer All, Recently, it seem to me that integrated seurat counts of RNA slot was not corrected yet and origin data, which make me confuse about data whether should take sample-corrected firstly or not when runing singler? Any advice would be grateful

dtm2451 commented 4 years ago

The "RNA" slot is typically better than the "integrated" slot, and either raw or normalized counts data work fine for test. (ref should be normalized, but test does not need to be.)

Not sure if that answers your question?

dtm2451 commented 4 years ago

closing as I think this is resolved. Feel free to open a new issue if question(s) remain.