Question: Error in FindTransferAnchors Seurat
0
gravatar for massonix
10 days ago by
massonix0
massonix0 wrote:

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 scrna-seq • 65 views
ADD COMMENTlink written 10 days ago by massonix0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 934 users visited in the last hour