Hi! I am trying to run scone() on a very small expression dataset (~2000 genes and 15 cells) to test out my user-defined functions and see the results. I ran into the following error, which I don't know how to resolve:
Error: BiocParallel errors
element index: 4, 5, 6, 7, 8, 9, ...
first error: NA/Inf/NaN Expression Values.
The expression data were pre-preprocessed and I removed genes that were not expressed in the cells. My scaling list includes user-defined functions for a few normalization methods (Seurat's simple norm, sctransform's vst(), SCnorm, and scran). The user-defined functions (besides scran) all return the normalized matrices, not scaled. My user-defined functions return normalized matrices when I call them on their own.
This is how I am calling the scone() function:
BiocParallel::register(BiocParallel::SerialParam())
my_scone <- scone(my_scone,
scaling=scaling,
run=TRUE,
eval_kclust = 2:6,
k_ruv = 0,
k_qc = 2,
return_norm = "in_memory",
zero = "postadjust",
adjust_bio="no",
adjust_batch="no",
bpparam = BiocParallel::SerialParam(),
verbose = TRUE)
How could I resolve this error? Thank you!
Hi! I am trying to run scone() on a very small expression dataset (~2000 genes and 15 cells) to test out my user-defined functions and see the results. I ran into the following error, which I don't know how to resolve:
The expression data were pre-preprocessed and I removed genes that were not expressed in the cells. My scaling list includes user-defined functions for a few normalization methods (Seurat's simple norm, sctransform's vst(), SCnorm, and scran). The user-defined functions (besides scran) all return the normalized matrices, not scaled. My user-defined functions return normalized matrices when I call them on their own.
This is how I am calling the scone() function:
How could I resolve this error? Thank you!