Question: CATALYST - Debarcoding visualisation error
0
gravatar for ammasakshay
12 days ago by
ammasakshay30
ammasakshay30 wrote:

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.

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