ERROR reading h5 output in R about cellbender HOT 2 CLOSED

Hi @sjfleming, thank you for the response!

It appears there was something corrupt about the file I was trying to read in with Seurat - the outputs from all my other libraries seem to work. Apologies!

The "DelayedMatrix" appears to be a new direction that the developers of many Bioconductor single-cell packages are taking (https://osca.bioconductor.org/), whereas the count matrices were previously stored as "dgCMatrix" in the single cell experiment S4 objects. I guess I need to learn how to handle these now...!

Thank you for the interesting work!

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Hi @ONeillMB1, thanks for trying out CellBender!

I have not tried opening the output files using read10xCounts() from DropletUtils, but I will check on that.

As for Seurat, that has been tested quite a bit. Seurat 2 and 3 should all be able to open the CellBender h5 output files using something like

# load Seurat (version 3) library
library(Seurat)

# load data from the filtered h5 file
data.file <- 'file_name_out_filtered.h5'
data.data <- Read10X_h5(filename = data.file, use.names = TRUE)

# create Seurat object
obj <- CreateSeuratObject(counts = data.data)

It looks like you may have been running into an error that was related to file permissions.

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