Hello, I have a singlecell dataset composed by 8 clusters in a Seurat object that I converted into a Singlecellexperiment following the indications in the SingleR book. I annotated it on a reference dataset with the following parameters:
table(subset_c2_sce$RNA_snn_res.0.5)
0 1 2 3 4 5 6 7
483 453 382 366 335 243 228 122
pred.subset <- SingleR(test = Counts, ref = subset_c2_sce, labels = subset_c2_sce$RNA_snn_res.0.5,
de.method = "wilcox")
table(pred.subset$pruned.labels)
0 1 3 7
59 157 1529 188
to.remove<- pruneScores(pred.subset, min.diff.med = 0.05)
# Create pruned labels
pruned_labels <- pred.subset$labels
pruned_labels[to.remove] <- "NI"
# Assign pruned labels to the metadata
tbx1$singleR <- as.factor(pruned_labels)
table(tbx1$singleR)
0 1 3 7 NI
5 107 1147 14 660
My question is... why the clusters 2-4-5-6 have not been annotated?
I tried to annotate them on another dataset, and again, there are only the labels of clusters 0-1-3-7
Thank you in advance
Hello, I have a singlecell dataset composed by 8 clusters in a Seurat object that I converted into a Singlecellexperiment following the indications in the SingleR book. I annotated it on a reference dataset with the following parameters:
My question is... why the clusters 2-4-5-6 have not been annotated?
I tried to annotate them on another dataset, and again, there are only the labels of clusters 0-1-3-7
Thank you in advance