Entering edit mode
4.8 years ago
massonix
▴
20
I have a scRNA-seq that I want to annotate using the Linnarson's brain cell atlas. To that end, I am using the Label Transfer pipeline from Seurat, which you can find here: https://satijalab.org/seurat/v3.0/pancreas_integration_label_transfer.html . This is my code:
# Connect to loom object
brain_loom <- connect(filename = "data/TM_brain_ref.loom")
brain_loom
# Convert to Seurat
brain_seu <- as.Seurat(brain_loom)
# Pre-processing
brain_seu <- NormalizeData(
object = brain_seu,
normalization.method = "LogNormalize",
scale.factor = 10000,
display.progress = TRUE
)
brain_seu <- FindVariableFeatures(brain_seu, selection.method = "vst", nfeatures = 2000)
brain_seu <- ScaleData(brain_seu)
brain_seu <- RunPCA(brain_seu, features = VariableFeatures(object = brain_seu))
saveRDS(brain_seu, "results/R_objects/brain_reference_Seurat.rds")
# Project data
anchors <- FindTransferAnchors(reference = brain_seu, query = epid_seu, dims = 1:30)
However, when executing the FindTransferAnchors() function, I get the following error:
Performing PCA on the provided reference using 2000 features as input.
Projecting PCA
Error in FastSparseRowScaleWithKnownStats(mat = proj.data, mu = feature.mean, :
Not an S4 object.
Do you have any idea on what is the underlying problem?
Thanks a lot!