Error when anndata to seurat

cellgeni / sceasy

A package to help convert different single-cell data formats to each other

GNU General Public License v3.0

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Error when anndata to seurat #45

Open GouQiao opened 2 years ago

GouQiao commented 2 years ago

Hi,

I want to convert h5ad to seurat.

sceasy::convertFormat("scTCR.h5ad", from="anndata", to="seurat",

outFile='scTCR.rds') But I had error: Error in dimnamesGets(x, value) : invalid dimnames given for “dgCMatrix” object

Do you know how to solve it?

Gou

JarningGau commented 2 years ago

I also met the same problem. My solution here: Downgrade your scipy package from 1.8.0 to 1.7.1

reticulate::py_install(packages = c("scipy==1.7.1"))

ZunpengLiu commented 1 year ago

Ah, I also got the similar error: `Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 't': invalid class “dgCMatrix” object: 'x' slot is not of type "double"

`

I have not figured out how to resolve it.

YiweiNiu commented 11 months ago

@ZunpengLiu Hi, I solved this by downgrading the anndata package. Please see this thread for more information: https://github.com/mojaveazure/seurat-disk/issues/109