Error in FindTransferAnchors Seurat
0
0
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!

Seurat seurat scRNA-seq • 2.5k views
ADD COMMENT

Login before adding your answer.

Traffic: 2826 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6