I previously worked with SingleR and Seurat to annotate my clusters. I have followed the workflow stated here and it all worked fine.

The Seurat object is already scaled and normalized.

Now, when trying to do it again, with the same data set,:

sce <- as.SingleCellExperiment(seurat_starsolo)
ref <- cells_highquality_ovary.sce
pred <- SingleR(test=sce, ref=ref, labels=ref$ident, method = "wilcox", clusters = colData(sce)$ident)

seurat_starsolo[["SingleR.labels"]] <- pred$labels

it throws an error:

Error: Cannot add more or fewer cell meta.data information without values being named with cell names

I don't understand why it's not working no, that I haven't change anything.

any help would be appreciated.

I have found the problem, but this still doesn't explain the behaviour or the present error.

The clusters arguments says: A character vector or factor of cluster identities for each cell in test. If set, annotation is performed on the aggregated cluster profiles, otherwise it defaults to per-cell annotation.

This makes the analysis much faster, but yields a data frame with one row for each level of clusters. As I have 32 clusters in my original Seurat object, it outputs a data frame with 32 rows. Now the problem is to map these labels back to my Seurat object.