Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq and Spatial Transcriptomics data.
While running bcRegressOut(), it stops with the following error:
k.neighbors must be lower than the number of complete cases in @normalized slot: 0.
The data I'm working with have a high proportion of NA and all samples have at least one missing value. I was indicated to replace these missing values by 0, meaning no enrichment for that drug signature, and recompute values, step after which regression worked well.
# Replace NAs by 0s
bc@normalized[is.na(bc@normalized)] <- 0
bc <- bcRecompute(bc, slot = "normalized")`
While running
bcRegressOut()
, it stops with the following error:The data I'm working with have a high proportion of NA and all samples have at least one missing value. I was indicated to replace these missing values by 0, meaning no enrichment for that drug signature, and recompute values, step after which regression worked well.
Thanks for the support!