Not all batches have at least 'neighbors_within_batch' cells in them.

[parkjooyoung99]

Hello,
I am running bbknnR with code below
bbknnR::RunBBKNN(kera, batch=c('condition','dataset'))

where I get the error below

Running BBKNN using RcppAnnoy...
Error in bbknn_annoy(pca = object, batch_list = batch_list, neighbors_within_batch = neighbors_within_batch, :
Not all batches have at least 'neighbors_within_batch' cells in them.

Can anyone help me to figure out the problem??

Thanks!

[WhatMelonGua]

maybe there is a batch includes very fewer cells occur that?I meet this question,too.

[yuanG2000]

did you figure out? I meet the same problem.

[mjesse-github]

I had the same issue (in the Python version), I set a threshold, which fixed it. Previously there was a sample with 2 cells...

adata = sc.read(INFILE)

print(adata.obs["Donor"].value_counts())

min_cells = 10
vc = adata.obs["Donor"].value_counts()
keep = vc[vc >= min_cells].index
adata = adata[adata.obs["Donor"].isin(keep)].copy()

print(adata.obs["Donor"].value_counts())