Error in RANN::nn2

[S Hui]

Hello,

I am getting the following error when running the train_classifier function:

> classifier <- train_cell_classifier(cds = train_cds,

+                                          marker_file = marker_file_path,

+                                          db="none",#org.Hs.eg.db,

+                                          cds_gene_id_type = "SYMBOL",

+                                          num_unknown = 500,

+                                          marker_file_gene_id_type = "SYMBOL",

+                                          return_initial_assign =F)

There are 19 cell type definitions

...

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

I wonder what the problem might be and how to fix it?

Thanks for your help,

Shui

[Hannah Pliner]

That error looks like there aren't enough cells to compute a nearest neighbors tree. Are you running with a very small number of cells?