CreateSinglerSeuratObject error from raw reads

[jrnick7]

Hi,

I encountered an error when running CreateSinglerSeuratObject as following, could you help me look into it? This raw dataset works for Seurat cluster but not work here.

Thanks a lot.

`

MCF7_singleR = CreateSinglerSeuratObject(sm, annot = NULL, "mcf7_singleR",
                                    min.genes = 300, technology = "10X", species = "Human" , citation = "",
                                    ref.list = list(), normalize.gene.length = F, variable.genes = "de",
                                    fine.tune = T, reduce.file.size = T, do.signatures = T, min.cells = 5,
                                    npca = 10, regress.out = "nUMI", do.main.types = T,
                                    reduce.seurat.object = T, numCores = SingleR.numCores)

"Create Seurat object..."
Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-')
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 4344
Number of edges: 165222

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.7660
Number of communities: 10
Elapsed time: 0 seconds
[1] "Creat SingleR object..."
[1] "Dimensions of counts data: 29134x4344"
[1] "Annotating data with HPCA..."
[1] "Variable genes method: de"
[1] "Number of DE genes:0"
[1] "Number of cells: 4344"
**Error in if (xor(((x[n] - mean(x)) < (mean(x) - x[1])), opposite)) { : 
  argument is of length zero**
In addition: There were 50 or more warnings (use warnings() to see the first 50)`

[dviraran]

The names in your count data are probably not gene symbols so SingleR can't identify genes to use ("Number of DE genes:0").

Best, Dvir