Error: Column `cell_type` is not found

[jamesonholloman]

Hi,

Thanks so much for this helpful tool! When I analyze my single nuclei dataset, I'm able to run pseudobulk and mixed model analyses through Libra but when I attempt to run a single cell analysis I receive an error message. I've listed two examples of code below demonstrating the successful running of the pseudobulk analysis and the error I receive with single cell.

DE = run_de(oligos, meta = meta, de_family="pseudobulk",de_method="limma",de_type="voom")
[1] "1"

DE = run_de(oligos, meta = meta, de_family="singlecell",de_method="wilcox")
Normalizing layer: counts
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[1/1] working on cell type: 1 ...
object 'method' not foundError in group_by():
! Must group by variables found in .data.
✖ Column cell_type is not found.

Any thoughts on why this is occurring?

[AlanTeoYueYang]

Hi, there was a minor bug that has been fixed.

[jamesonholloman]

Thanks for the reply! Unfortunately, I'm still getting the same error. I ran the check inputs function on my data and there were no errors so no sure what's causing the issue.

DE = run_de(d, de_family = 'pseudobulk', de_method = 'edgeR', de_type = 'QLF')
[1] "oligos"
DE = run_de(d, de_family = 'singlecell', de_method = 'wilcox')
Normalizing layer: counts
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[1/1] working on cell type: oligos ...
object 'method' not foundError in group_by():
! Must group by variables found in .data.
✖ Column cell_type is not found.
Run rlang::last_trace() to see where the error occurred.

[igrisch]

I am having the same problem, even with the most updated version.

[dbyzy]

I also have the same problem

[AlanTeoYueYang]

Hi all,

Do you mind sharing with me your datasets so I can figure what might be wrong?

Best,
Alan