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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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h5ad to Seurat conversion "AttributeError: 'dict' object has no attribute 'dtype'" #77

Open jestlin15 opened 1 year ago

jestlin15 commented 1 year ago

Hi, I am trying to convert a h5ad file to Seurat object but am faced with this error can I please please get some help.

This is my inout code : sceasy::convertFormat("GSE175533_sceasy_hay.h5ad", from="anndata", to="seurat", outFile='GSE175533_sceasy_hay.rds')

Python Exception Message Traceback (most recent call last): File "/python3.9/site-packages/anndata/readwrite/read.py", line 447, in read_h5ad File "/python3.9/site-packages/anndata/readwrite/read.py", line 502, in _read_args_from_h5ad File "/python3.9/site-packages/anndata/core/anndata.py", line 2157, in _args_from_dict AttributeError: 'dict' object has no attribute 'dtype'

── R Traceback

  1. sceasy::convertFormat(...)
  2. sceasy (local) func(obj, outFile = outFile, main_layer = main_layer, ...)
  3. anndata$read_h5ad(inFile)
  4. reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)

R version 4.1.2

GSE h5ad Data download from : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE175533

lisch7 commented 11 months ago

same issue

TamiaChin commented 1 month ago

This is an issue concerning anndata package. conda install "anndata>=0.7" -c conda-forge It should fix