Error in GenerateCellHashingCalls(barcodeMatrix = hashtag_counts, methods = methods) : Unknown method: bff_threshold

[lucygarner]

Hi,

I am trying to follow the benchmarking vignette but am getting an unknown method bff_threshold error with GenerateCellHashingCalls.

hashtag_counts <- as.matrix(GetAssayData(seurat_obj, assay = "HTO", slot = "counts"))
methods <- c("bff_cluster", "bff_threshold", "gmm_demux", "multiseq", "htodemux", "dropletutils")
df <- GenerateCellHashingCalls(barcodeMatrix = hashtag_counts, methods = methods)

[1] "Starting BFF" [1] "rows dropped for low counts: 1 of 6" [1] "Running BFF_cluster" [1] "Doublet threshold: 0.05" [1] "Neg threshold: 0.05" [1] "Min distance as fraction of distance between peaks: 0.1" [1] "Thresholds:" [1] "HTO13: 33.7056078381879" [1] "HTO12: 73.7157064313985" [1] "HTO10: 90.3668786271235" [1] "HTO9: 115.875740004405" [1] "HTO7: 188.933809112811" [1] "Smoothing parameter j = 5" [1] "Smoothing parameter j = 10" [1] "Smoothing parameter j = 15" [1] "Smoothing parameter j = 20" [1] "Smoothing parameter j = 25" [1] "Smoothing parameter j = 30" [1] "Smoothing parameter j = 35" [1] "QuartzBitmap_Output - unable to open file '/Users/lucy/Documents/2022/devel/10x/R/.Rproj.user/shared/notebooks/B6950FE2-hto_demultiplexing_v2/1/4AC24CAF8B338E39/cwzhkqd5gl65e_t/_rs_chunk_plot_002.png'" 1: GenerateCellHashingCalls(barcodeMatrix = hashtag_counts, methods = methods)

Error in GenerateCellHashingCalls(barcodeMatrix = hashtag_counts, methods = methods) : Unknown method: bff_threshold Error in dev.off() : QuartzBitmap_Output - unable to open file '/Users/lucy/Documents/2022/devel/10x/R/.Rproj.user/shared/notebooks/B6950FE2-hto_demultiplexing_v2/1/4AC24CAF8B338E39/cwzhkqd5gl65e_t/_rs_chunk_plot_002.png'

Best wishes, Lucy

[bbimber]

Apologies - bff_threshold was renamed to bff_raw a long time ago (it's identical), and apparently the docs are out of date. I'll try to update this, but I think if you just change that to 'bff_raw' it will work.

[lucygarner]

Great thank you - this works.