Cannot find more nearest neighbours than there are points
mahermassoud opened this issue · 1 comments
mahermassoud commented
When I run train_cell_classifier()
on my dataset with my marker file, I get the following output.
> v3.classifier <- train_cell_classifier(cds=qc.hp.mono,
+ marker_file=MARKER.FP,
+ db=org.Hs.eg.db,
+ cds_gene_id_type="ENSEMBL",
+ num_unknown=200,
+ marker_file_gene_id_type="SYMBOL",
+ cores=4)
There are 21 cell type definitions
training_sample
B cell CD34+
500 77
Dendritic cell Endothelium
287 19
Fibroblasts/myofibroblasts Gastric epithelium
454 500
Gastric epithelium Antrum Gastric neuroendocrine cells
5 115
Gastric stem cell Macrophage
3 93
Monocyte NK cell
390 106
T cell Unknown
135 200
The following cell types do not have enough training cells and will be dropped: Gastric epithelium Antrum Gastric stem cell
Loaded glmnet 4.0-2
Model training finished.
Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, :
You're computing too large a percentage of total singular values, use a standard svd instead.
Error in RANN::nn2(pcs, pcs, k + 1, searchtype = "standard") :
Cannot find more nearest neighbours than there are points
In addition: Warning messages:
1: In make_name_map(parse_list, as.character(row.names(fData(norm_cds))), :
10 genes could not be converted from SYMBOL to ENSEMBL These genes are listed below:
2: In make_name_map(parse_list, as.character(row.names(fData(norm_cds))), :
The following genes from the cell type definitionfile are not present in the cell dataset. Pleasecheck these genes for errors. Cell typedetermination will continue, ignoring these genes.
PECAM1
CD3
CD11B
CD141
CD25
CD49D
TROY
CD16
CD15
CD25
GIF
3: In train_cell_classifier(cds = qc.hp.mono, marker_file = MARKER.FP, :
Cell type Neutrophil has no genes that are expressed and will be skipped
4: In train_cell_classifier(cds = qc.hp.mono, marker_file = MARKER.FP, :
Cell type Gastric parietal cells has no genes that are expressed and will be skipped
mahermassoud commented
Fixed by changing num_unknown=500
to num_unknown=1000