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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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CreateSinglerObject error #97

Open Zifeng-L opened 5 years ago

Zifeng-L commented 5 years ago

Hi,

I encountered an error when running CreateSinglerSeuratObject as following, could you help me look into it?


counts.table <- GetAssayData(object = S132TBU, slot = "counts")
annot.table <- S132TBU@meta.data$orig.ident
singler = CreateSinglerSeuratObject(counts.table,annot.table,S132TBU,
                                      min.genes = 200, technology = "10X", species = "Human",
                                      citation = "", ref.list = list(), normalize.gene.length = F,
                                      variable.genes = "de", fine.tune = T, reduce.file.size = T,
                                      do.signatures = F, min.cells = 2, npca = 10,
                                      regress.out = "nUMI", do.main.types = T, 
                                      reduce.seurat.object = T,temp.dir = NULL, numCores = SingleR.numCores)

An object of class Seurat 40104 features across 18239 samples within 2 assays Active assay: SCT (19399 features) 1 other assay present: RNA 2 dimensional reductions calculated: pca, umap [1] "Reading single-cell data..." [1] "Create Seurat object..." Error in unique.default(x, nmax = nmax) : unique() applies only to vectors

dviraran commented 5 years ago

Hi,

This is an error in Seurat, not SingleR. You can look at the CreateSeuratObject function code to follow the steps and identify where exactly is the error.

Best, Dvir