I'm Using the code found here - http://bioconductor.org/packages/release//bioc/vignettes/CATALYST/inst/doc/preprocessing.html#plotmahal-all-barcode-biaxial-plot
My debarcoding script looks like
``` #debarcode sce <- assignPrelim(sce, mat) # view barcode channels rownames(sce)[rowData(sce)$is_bc] # view number of events assigned to each barcode population table(sce$bc_id) # estimate separation cutoffs sce <- estCutoffs(sce) # view separation cutoff estimates metadata(sce)$sep_cutoffs #For each barcode, show the distribution of barcode separations #and yields upon debarcoding as a function of separation cutoffs. png('Barcode Seperation - All.png') plotYields(sce, which = c(0)) dev.off() #Take cutoff value from this plot. In this case we select -> 0.2 # use global / population-specific separation cutoff(s) sce2 <- applyCutoffs(sce) sce3 <- applyCutoffs(sce, sep_cutoffs = 0.2) # compare yields before and after applying # global / population-specific cutoffs c(specific = mean(sce2$bc_id != 0), global = mean(sce3$bc_id != 0)) # proceed with population-specific filtering sce <- sce2 # event plots for unassigned events # & barcode population D1 plotEvents(sce, which = c(0, "STING_B6"), n = 25) ```
The output returns the error
> # Normalized intensities for barcoding events > plotEvents(sce, which = c(0, "STING_B6"), n = 25) Error in bc_key[ids, ] : subscript out of bounds
I'm trying to figure out what it means and how to fix it. Thank you.