drisso/zinbwave

Scanpy AnnData Object as Input

Closed this issue · 3 comments

aditisk commented

Hello,

I am using Scanpy for analyzing our 10x data. Do you have any suggestions of how I could easily use data from Scanpy (AnnData object/h5ad format) as input in zinbwave ?

This is what I tried so far:

  • Converted from h5ad to Seurat object.

  • Converted this Seurat object to a SingleCellExperiement Object
    But when I try to use this SCE object, I get the following error message:

Error in .local(Y, ...) :
The input matrix should contain only whole numbers.

@drisso any thoughts on what the easiest way around this issue would be ? Any help from other users is highly appreciated.

Thank you.

drisso commented

Hi @aditisk

the error message suggests that your matrix does not contain counts but something else (i.e., non-integer values). Zinbwave must be applied to raw unnormalized counts, are you giving as input something different? E.g., normalized data?

aditisk commented

Hi @drisso, I’m so sorry I missed your comment above. I’ll try again with raw data. Thanks.

drisso commented

OK, happy to reopen this if you're still having issues.