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Error in Read10x with R Matrix package v. 1.5-0 #6438

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ms-gx opened this issue Sep 19, 2022 · 1 comment
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Error in Read10x with R Matrix package v. 1.5-0 #6438

ms-gx opened this issue Sep 19, 2022 · 1 comment
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@ms-gx
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ms-gx commented Sep 19, 2022 •
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When using function Read10x I got the following error:
Error: as(<dgTMatrix>, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "CsparseMatrix") instead

In function Read10x I changed
list_of_data[[j]] <- as(object = list_of_data[[j]], Class = "dgCMatrix")
to
list_of_data[[j]] <- as(object = list_of_data[[j]], Class = "CsparseMatrix")

Now it works, but I guess this has to be adjusted globally.

See here:
ms-gx@63185aa
@ms-gx ms-gx added the bug Something isn't working label Sep 19, 2022
@AustinHartman
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Thanks for raising this - Seurat 4.2.0 was just released on CRAN which addresses coercions which were deprecated in Matrix 1.5.0. Alternatively, you can try modifying the Matrix.warnDeprecatedCoerce option in order to toggle warnings/errors as described here under 1.5.0

@samuel-marsh samuel-marsh mentioned this issue Sep 26, 2022
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laurenhsu1 added a commit to laurenhsu1/CellChat that referenced this issue May 22, 2024
@laurenhsu1
Update CellChat_class.R
0e42f52 
I got an error when trying to feed the createCellChat function a SingleCellExperiment containing dgRMatrix format in logcounts. The error occurs in trying to coerce a dgRMatrix to dgCMatrix, but it works to coerce to "CsparseMatrix", which ultimately results in a dgCMatrix. 

Supposedly this issue has been resolved in zellkonverter a couple years ago, (theislab/zellkonverter#55), but I just ran into this today with data imported with zellkonverter which was a dgRMatrix, and my packages are up to date. I then found a couple other issues with discussion of this particular conversion problem, so I would suggest making this small update so that it will seamlessly work with dgRMatrix input too! 
theislab/zellkonverter#34
satijalab/seurat#6438
@laurenhsu1 laurenhsu1 mentioned this issue May 22, 2024
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@AustinHartman @ms-gx