Open shregeno8 opened 2 years ago
This is my example Sample sheet
Hi Shri, can you try individual
column values without underscores? e.g. pNF10
Hello Thanks for replying. I tried that and same error.
This will need patching, but a quick fix should be to make the manifest
column the first in the sample sheet.
So everything works well till this step(please see the photos which are in order)
This will need patching, but a quick fix should be to make the
manifest
column the first in the sample sheet.
I will try this and get back. Hoping that it works
Thanks
Hi I tried and unfortunately that doesn't work either.
Are you using the latest docker image (0.7.1)?
This is my example Sample sheet
Hi it worked. I had to change my group column in the sample sheet. So basically it does not accept duplicate group names. Strange because there could be cases where all the sample are from same cell lines , so don't really need to separate them by groups.
Thanks for filing the issue. Should be fixed in the next version!
Hi this is the log from the run
── Computing Uniform Manifold Approximation and Projection (UMAP) ──
✔ UMAP was computed successfully with PCA input ✔ Successfully added 2 reducedDim slots:
PCA, UMAP_PCA
✔ Pseudobulking completed (0.08 minutes taken). ✔ SingleCellExperiment successfully annotated with pseudobulk plots: • sce@metadata$pseudobulk_rd_plots$PCA • sce@metadata$pseudobulk_rd_plots$UMAP_PCA • sce@metadata$pseudobulk_plots$combined_heatmap _Error in.rowNamesDF<-
(x, value = value) : duplicate 'row.names' are not allowed Calls: annotate_merged_sce ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<- In addition: Warning message: non-unique values when setting 'row.names': ‘NA_pNF_AACGGGATCCATTTGT-1’, ‘NA_pNFAATTCCTTCTTGGTGA-1’,