Error on mapping query with reference
sidrahmaryam-cyber opened this issue · 0 comments
Hello,
I am trying to reproduce this tutorial using the data I have.
https://github.com/immunogenomics/symphony_reproducibility/blob/main/cancer_kidney/cancer.ipynb
However, when I am mapping the query to the reference,
query = mapQuery(query_exp, # query gene expression (genes x cells) query_metadata, # query metadata (cells x attributes) reference, # Symphony reference object do_normalize = TRUE, # perform log(CP10k) normalization on query do_umap = TRUE)
I get an error saying
Normalizing
Scaling and synchronizing query gene expression
Found 1795 out of 2000 reference variable genes in query dataset
Error in scaleRowsWithStats_dgc(A@x, A@p, A@i, mean_vec, sd_vec, ncol(A), :
Not compatible with requested type: [type=NULL; target=double].
In addition: Warning message:
Unknown or uninitialised column: stddev
.
Can you please let me know the possible reason and the solution.