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)`
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.
`