as.anndata isseu

[lindsdudley]

Hi Samuel,

Thank you so much for creating this incredibly useful package. I am trying to use it to transform a seurat object into an ann.data object to work with it in a python program. I have installed the development branch v2.1.2.9039 but I am still getting this error:

CEST_3_1_sc_ad <- as.anndata(x = CEST_3_1_sc, file_path = "~/", file_name = "CEST_3_1_sc_anndata.h5ad")
• Checking Seurat object validity
• Extracting Data from SCT assay to transfer to anndata.
The following columns were removed as they contain identical values for all rows:
ℹ orig.ident and sample_id
• Creating anndata object.
• Writing anndata file: "/home/lindseydudley/CEST_3_1_sc_anndata.h5ad"
Warning messages:
1: Adding a command log without an assay associated with it
2: Adding a command log without an assay associated with it

Please advise if there is anything that I can do.

[samuel-marsh]

Hi @lindsdudley,

Thanks for the kind words!! Are you getting an error of just the warnings? Those warnings in message above shouldn't be an issue.

Best,
Sam

[lindsdudley]

I'm so sorry you're right I was just saving it to the wrong place. Thank you so much for the prompt response and fix in the development version.

[samuel-marsh]

Great! No problem!