Entering edit mode
3.2 years ago
ammasakshay
▴
60
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.