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as.Seurat error converting sce with ?more recent CellRanger and CellBender .h5 files #4353

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JTpath opened this issue Apr 12, 2021 · 5 comments
Closed

as.Seurat error converting sce with ?more recent CellRanger and CellBender .h5 files #4353

JTpath opened this issue Apr 12, 2021 · 5 comments
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bug Something isn't working

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@JTpath
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JTpath commented Apr 12, 2021

Hi, I've been working with h5 files from cellbender on 10x data.

Previously I had no trouble going to and from single cell experiment format, but for the last few days I've been getting this error.

'Error in .subset2(x, i, exact = exact) : subscript out of bounds'

Converting pbmc_small to and from sce works fine, but data from the new v6 cellranger on the 10x website gives the same error (https://cf.10xgenomics.com/samples/cell-exp/6.0.0/Brain_3p_LT/Brain_3p_LT_filtered_feature_bc_matrix.h5)

Please help.
Thanks

library(Seurat)
#> Registered S3 method overwritten by 'spatstat.geom':
#>   method     from
#>   print.boxx cli
#> Attaching SeuratObject
library(hdf5r)

f1 <- "data/Brain_3p_LT_filtered_feature_bc_matrix.h5"
data.file <- Read10X_h5(filename = f1, use.names = TRUE)
#>Warning message:
#>In sparseMatrix(i = indices[] + 1, p = indptr[], x = as.numeric(x = counts[]),  :
#>  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
data <- CreateSeuratObject(counts = data.file)
data.sce <- as.SingleCellExperiment(data)
data.seu <- as.Seurat(data.sce)
#>Error in .subset2(x, i, exact = exact) : subscript out of bounds

Created on 2021-04-12 by the reprex package (v2.0.0)

Session info 
sessioninfo::session_info()
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#> [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
@JTpath JTpath added the bug Something isn't working label Apr 12, 2021
@JTpath
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JTpath commented Apr 14, 2021

Switched to the master version rather than the latest dev release and it works again.

@saketkc saketkc closed this as completed Apr 16, 2021
@ka-lw
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ka-lw commented Jun 2, 2021

Hi I'm getting the same issue - Seurat version Seurat_4.0.2
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

I've tried using Seurat_4.0.1 with no luck.

@saketkc
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saketkc commented Jun 2, 2021

This has been recently fixed in the develop branch. You can try updating Seurat to the latest dev version using the instructions here

@ka-lw
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ka-lw commented Jun 2, 2021

Nice, that's sorted it. Thanks for all your hard work guys.

@JTpath
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JTpath commented Jun 2, 2021

This has been recently fixed in the develop branch. You can try updating Seurat to the latest dev version using the instructions here

Awesome! Thanks

I suspect I've duplicated this issue in #4549, I'll close it

@JTpath JTpath mentioned this issue Jun 2, 2021
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