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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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negative length vectors are not allowed : Error when converting anndata to seurat #75

Open bapoorva opened 1 year ago

bapoorva commented 1 year ago

Hi,

I've used sceasy before with no issues. But this time, i tried to convert an h5ad file to a seurat object and got this error

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 't': negative length vectors are not allowed

This is my code

library(sceasy)
library(reticulate)
use_python('/Users/bapoorva/miniconda3/bin/python3')
loompy <- reticulate::import('loompy')

sceasy::convertFormat("~/HLCA/local.h5ad", from="anndata", to="seurat",
                      outFile='HLCA_humanref.RDS')

I downloaded the h5ad from this link. It is the human reference file from the Human Lung Cell Atlas (HLCA)

Any ideas on how to resolve this ?

Thanks

AlexandrePelletier commented 8 months ago

I got the same error, anyone have been able to fix it ?