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neurorestore / Augur

Cell type prioritization in single-cell data
MIT License
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the error of Augur #23

Open crystal0721 opened 1 year ago

crystal0721 commented 1 year ago

hi, we test augur using our data. the code as follows:

seurat.obj<-readRDS('zsh_subset.rds') augur = calculate_auc(seurat.obj,cell_type_col = "stim", label_col = "seurat_clusters")

while we got the errors:

using default assay: RNA ... Error in calculate_auc(seurat.obj, cell_type_col = "stim", label_col = "seurat_clusters") : no cell type had at least 20 cells in all conditions Execution halted

we want to know how to know the reason and how to solve. Thanks for your help and we are looking for your replay.

skinnider commented 1 year ago

As the error suggests, there are no cell types with at least 20 cells in all conditions. It seems to me from the code provided that you may be swapping the cell type and label columns in Augur's arguments.

crystal0721 commented 1 year ago

Thanks for your apply. Yes, we swapped the cell type and label columns in Augur's arguments. While the number of cells under each condition is more than 20，one is 6413，the other is 3764.