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constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
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plotMarkerDistribution(sc) error #26

Closed chansigit closed 4 years ago

chansigit commented 4 years ago

Can you please tell me what are the possible bugs with my code?

plotMarkerDistribution(sc)

Error in estimateNonExpressingCells(sc, as.list(gns), ...): Invalid cluster specification.  clusters must be a named vector with all column names in the table of counts appearing.
Traceback:

1. plotMarkerDistribution(sc)
2. inferNonExpressedGenes(sc, ...)
3. estimateNonExpressingCells(sc, as.list(gns), ...)
4. stop("Invalid cluster specification.  clusters must be a named vector with all column names in the table of counts appearing.")
cswoboda commented 4 years ago

Hey, Happy to help but will need session info and more details. It looks like an issue with the formatting of your Seurat_DR object. Could you show me the code for that object? Casey

chansigit commented 4 years ago

I find the reason: the cells supplied by seurat object is filtered when CreateSeuratObject but SoupX read cells from cellranger filtered data. their nRow conflict with each other.