Error in barcodeData; Incorrect number of dimensions

[mbassalbioinformatics]

hi, im trying to run the processCountMatrix function but keep coming up with the following error

10X data contains more than one type and is being returned as a list containing matrices of each type.
Error in barcodeData[which(!(rownames(barcodeData) %in% barcodeBlacklist)),  : 
  incorrect number of dimensions

Ive tried running the following commands, all result in exactly the same error

barcodeData <- ProcessCountMatrix(rawCountData = './', 
                                  minCountPerCell = 5, 
                                  barcodeWhitelist = c('HTO1', 'HTO2', 'HTO3'))

barcodeData <- ProcessCountMatrix(rawCountData = './', 
                                  minCountPerCell = 5, 
                                  barcodeWhitelist = c('HTO1', 'HTO2', 'HTO3'),
                                  barcodeBlacklist = "no_match")

barcodeData <- ProcessCountMatrix(rawCountData = './', 
                                  minCountPerCell = 5, 
                                  barcodeWhitelist = c('HTO1', 'HTO2', 'HTO3'),
                                  barcodeBlacklist = "unmapped")

barcodeData <- ProcessCountMatrix(rawCountData = './', 
                                  minCountPerCell = 5, 
                                  barcodeWhitelist = c('HTO1', 'HTO2', 'HTO3'),
                                  barcodeBlacklist = "total_reads")

barcodeData <- ProcessCountMatrix(rawCountData = './', 
                                  minCountPerCell = 5, 
                                  barcodeWhitelist = c('HTO1', 'HTO2', 'HTO3'),
                                  barcodeBlacklist = NULL)

Any suggestions/ideas as to what im doing wrong?

The current path (./) contains the following files

matrix.mtx.gz
barcodes.tsv.gz
features.tsv.gz

Much appreciated!

[bbimber]

I believe this is showing that cellranger was run in a mode that stores the gene expression, hashing, etc. together. See that message here:

https://www.10xgenomics.com/resources/analysis-guides/tag-assignment-of-10x-Genomics-cellplex-data-using-seurats-htodemux-function

You can also see it from ?Seurat::Read10X. I think I have a fix for this here: https://github.com/BimberLab/cellhashR/pull/115/files

Would you mind installing this version and seeing if it fixes your problem? Note, when you run this version it should detect that the incoming data are multi-assay. It will report the names of those assays and then stop. You can provide the datatypeName argument to ProcessCountMatrix(), and I think it will then work fine.

devtools::install_github(repo = 'bimberlab/cellhashR', ref = 'multiassay')

[mbassalbioinformatics]

Yep! For now seems to be sorted.

Very much appreciated to see bioinformatics tools that are being well supported. Also, very much appreciated how quickly you dealt with this issue!

[bbimber]

No problem. This is merged into the main branch so you or anyone who reads this in the future can use that.

[domenico-somma]

Hello, thanks for this very useful tool! I was wondering if you can release a new package version of this (1.0.4 maybe?) with this update. Would be great to keep track what version we have installed on our server.

Thanks

[bbimber]

sure, done