Help with Error: None of the requested features were found: PECAM1 in slot data

Question

[Chris]

Hi all, I decrease the resolution to get fewer clusters however I got the error when run:

FeaturePlot(object_combined, features = c('PECAM1'), min.cutoff = 'q10')
Error: None of the requested features were found: PECAM1 in slot data

Would you please have a suggestion? I don't have the error when keep high resolution. I appreciate it.

Answer 1

[bk11]

Can you check the available assays in your object_combined?

Assays(merged_seurat)
#it may show you as `predicted_ADT`, `RNA` etc. data slots
#your gene could in different assay, if it is not in predicted_ADT for example it could be in RNA data slot
DefaultAssay(merged_seurat) <- "RNA"

[Chris]

I think it is:

[1] "RNA"  "ATAC" "SCT"

[bk11]

I would recommend you to check in each data slots.

[Chris]

When I run DefaultAssay(object_combined) <- "RNA", the error has gone. Thank you!

[Chris]

when I choose SCT as DefaultAssay instead of RNA. the FeaturePlot is very different. Would you please have a comment? I found this one but still not clear: Seurat3: RNA vs SCT assays for DotPlot