problem with classify_cells results

[An Lau]

Hi, 

I'm trying to classify my own single cells data set using garnett,

but the results confuse me.

1. cluster_ext_type is the same as cell_type

2. the cell type in one garnett cluster is different 

as the pic above, how should I to know which cell type that cluster 1 belongs to ?

Thanks, 

An

[An Lau]

Picture display is not normal,  I upload once again

[Hannah A Pliner]

Hi An,

The cell_type assignments are clustering-independent. The cluster_ext_types are a post-processing step that extends the cell_type assignments when that makes sense. In your case, the cluster_ext_types are the same as cell_type because there is mixed assignment within the cluster. This may be because the clustering procedure has failed and the cells in cluster 1 are of multiple types - Garnett uses default clustering settings that won't work for all datasets. If you have clustering results from elsewhere, you can rerun the Garnett classification step using those clusters by setting pData(cds)$garnett_cluster to those cluster labels prior to the run.

Hope this helps,

Hannah

Hannah Pliner, Ph.D.

Lead Data Scientist for Single Cell Genomics

Brotman Baty Institute for Precision Medicine

Health Sciences Building (HSB) H564E

Seattle, WA

206-616-0454

hpl...@uw.edu

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[An Lau]

Hi Hannah,

Thank you for the clarification. 

I will try it.

An

Hannah A Pliner <hpl...@uw.edu> 于2019年6月5日周三 上午12:24写道：