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campbio / celda

Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data
http://bioconductor.org/packages/celda
MIT License
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Is it necessary to filter gene or cell filter needed after DecontX #391

Closed MISAKA-DaYu closed 1 year ago

MISAKA-DaYu commented 1 year ago

In Seurat vignettes, we often filter gene and features in CreateSeuratObject.

pbmc <- CreateSeuratObject(counts = pbmc.data, project = "pbmc3k", min.cells = 3, min.features = 200)

Do we still need to do the filter after running DecontX?

joshua-d-campbell commented 1 year ago

Hi @MISAKA-DaYu, thanks for trying out our tool. Yes, should still do all of the same filtering you would normally do. DecontX returns a raw count matrix where the ambient RNA has been subtracted out. All of the other filtering and analysis methods can be applied to this matrix as normal. I am going to move this to a Discussion for future reference.